The Sheffield Conference on Cheminformatics is always one of the highlights of the calendar, it will be held at The Edge, University of Sheffield, UK, Monday 19th – Wednesday 21st June, 2023. https://cisrg.shef.ac.uk/shef2023/.

As usual a great lineup of speakers

Confirmed Attendees & Titles of Paper:

• Adele Hardie A World of Probabilities: An sMD/MSM Approach for Rational Design of Allosteric Modulators
• Aras Asaad Persistence homological statistical summaries for ligand-based virtual screening
• Benoit Baillif Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
• Dan Woodward Coverage Score: A Model Agnostic Method to Efficiently Explore Chemical Space
• David Palmer Simultaneous Entropy, Enthalpy and Free Energy Prediction using a Physics-Informed Neural Network and Multi-task Learning
• Lauren Reid SARkush®: Automated Markush-like structure generation using matched pairs and generic atom scaffolds
• Helle van den Maagdenberg QSPRpred: a Flexible and Open Quantitative Structure-Property Relationship Modelling Tool
• Henriette Willems PI5P4K subtype-selective inhibitors: three binding modes from one privileged motif
• James Webster An in-silico benchmarking platform for generative de novo drug design
• Marc Lehner Partial Charge Prediction and Pattern Extraction from a AttentiveFP Graph Neural Network
• Maria J Falaguera Illuminating the Chemical Space of Untargeted Proteins
• Matteo Ferla Fragmenstein: stitching compounds together
• Maximilian Beckers Prediction of small molecule developability using large-scale in silico ADMET models
• Moritz Walter Integrating heterogeneous assay data for ML-based ADME prediction
• Noel O’Boyle Handling large chemical spaces in Structure-Based Drug Design
• Rajarshi Guha Virtual Screening of Virtual Libraries using a Genetic Algorithm
• Richard Gowers The Open Free Energy Consortium: Alchemistry for everyone
• Richard Sherhod Glolloc: a global-local mixture of experts model and its application to small molecule drug discovery
• Roger Sayle FNGRPRNTS: Processing just the bits you need, and none of the 1s you don’t.
• Roxana-Maria Rujan Resolving code names to structures from the medicinal chemistry literature: not as FAIR as it should be
• Samuel Genheden AiZynthFinder: developments and learnings from three years of industrial application
• Sébastien Guesné Beyond balanced accuracy: balanced Matthews’ correlation coefficient.
• Sohvi Luukkonen DrugEx: deep learning for de novo drug design — a case for A2B selective ligands
• Srijit Seal PKSmart: An Open-Source Computational Model to Predict in vivo Pharmacokinetics of Small Molecules
• Tuomo Kalliokoski Efficient structure-based virtual screening of ultra-large enumerated chemical spaces using macHine leArning booSTEd dockiNg (HASTEN)
• Uschi Dolfus Full modification control over retrosynthetic routes for guided optimization of lead structures

A really detailed account of how to set up an Apple Silicon MacBook under macOS Ventura 13.1 for computational materials science. https://aronwalsh.github.io/applesilicon/.

There is also useful update on Crystallography on MacOS https://scottlab.ucsc.edu/xtal/wiki/index.php/CrystallographyonOS_X. It is also worth noting https://subversion.xray.aps.anl.gov/trac/pyGSAS.

I've already detailed Setting up ML and AI tools on Apple Silicon https://www.macinchem.org/reviews/AIML/SettingAIML.php.

The latest RSC CICAG newsletter is now available http://www.rsccicag.org/indexhtmfiles/CICAG%20Newsletter%20Winter%202022-23%20FINAL.pdf.

This is a really bumper issue

Contents Chemical Information and Computer Applications Group Chair’s Report
CICAG Planned and Proposed Future Meetings
Social Media Migration – Opening up Mastodon as a Tool for Scholarly Communication
Cheminformatics: A Digital History ‒ Part 2. A Personal Perspective of the Role of the Web During the Period 1993-1996
InChI Technical Developments
Update from the Royal Society of Chemistry Library
The Open Free Energy Project
Meeting Report: SCI-RSC Workshop on Computational Tools for Drug Discovery 2022
A Crystallography Papermill: The CSD Response
Meeting Report: Ultra-Large Chemical Libraries
Open Science in the Royal Society of Chemistry
The Davy Notebooks Project
This JACS Does Not Exist: Generating Chemistry Abstracts with Machine Learning
Meeting Report: RSC-CICAG and RSC-BMCS 5th Artificial Intelligence in Chemistry Conference.
EU-OPENSCREEN ERIC: an Open-access Research Infrastructure for Chemical Biology and Early Drug Discovery
DECIMER ‒ An Open Toolkit for Optical Chemical Structure Recognition and Document Analysis
Cryo-EM for Industrial-Scale Structure-Based Drug Design
Cryo-EM & Drug Discovery
2022 CSD Updates
News from ACS CINF
News from CAS
RSC Databases Update
UKeiG: Winners of the Prestigious Tony Kent Strix Award 2022
AI4SD News
Book Review: Digital Transformation: New Tools and Methods for Mining Technological Intelligence
Cheminformatics and Chemical Information Books
2022 Reflections on Life at the Catalyst Science and Discovery Centre and Museum in Widnes
Other Chemical Information News

Contributions to the CICAG Newsletter are welcome from all sources ‒ please send to the Newsletter Editor Dr Helen Cooke FRSC: email helen.cooke100@gmail.com

When you renew your Royal Society of Chemistry membership you can choose “Chemical Information and Computer Applications Group” (group 86) as one of your groups to be a member of. Use the “Connecting with others” button at https://members.rsc.org/ If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141)

News just in from ChimeraX team https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html.

We are making a version of our ChimeraX molecular graphics program that runs natively on Apple's new M1 CPUs for faster interactive calculations. We'll report some speed-up timings and describe difficulties porting from Intel to the Apple M1 CPU. A native Apple M1 version of ChimeraX is not yet available, but we expect to release it within 6 months.

Difficulties porting ChimeraX to Apple M1 CPUs

• ChimeraX Python and C++ code needs no changes.
• ChimeraX uses 90 packages developed by others.
• 60 are pure Python from the PyPi repository.
• 30 are binary packages that need Apple M1 versions.
• 6 binary packages do not have Apple M1 distributions: ambertools, h5py, imagecodecs, netcdf4, pytables, scipy.
• Qt 6 window toolkit is distributed for Apple M1 but not Qt 5.
• ChimeraX uses Qt 5, the stable Qt version from 2012 - 2021.
• Qt 6 with html support was released September 2021.
• Apple M1 applications must be either all native M1 binaries or all Intel binaries, no mixing.
• Need to distribute either a large univeral package that includes both Intel and M1 binaries, or two separate ChimeraX versions.

Potential advantages of native Apple M1 ChimeraX

• Better OpenGL driver stability with Apple M1 GPU.
• No graphics driver crashes among 43 ChimeraX bug reports in 2021 with Apple M1.
• About 100 ChimeraX graphics driver crashes reported on Intel Macs in past 2 years.
• Better C++ crash stack traces with native M1 app than with Intel emulation.
• Intel ChimeraX crashes on M1 often give no C++ stack trace.

The 2022.02 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a variety of new features, including support for Apple Silicon!

This update also includes

• Browser-based Combinatorial Library Enumeration with on-the-fly reagent search and library generation

• MOEsaic Docking calculations with real-time visualization of results

• scFv and custom antibody homology models

• GPU-accelerated protein modeling and protein-protein docking

• Hydrogen Mass Repartitioning for accelerating MD and Thermodynamic Integration

• Database Viewer SNFG carbohydrate display, graphic objects, and enhanced plotting

If you want to read more about the performance gains using MOE on an M1 Mac have a look at this page https://www.macinchem.org/reviews/MacBooks/moe.php.

The RSC CICAG newsletter is now available

http://www.rsccicag.org/indexhtmfiles/CICAG%20Newsletter%20Summer%202022%20FINAL pdf

Chemical Information and Computer Applications Group Chair’s Report 4
Your CICAG Committee - Introducing Our New Members 5
CICAG Planned and Proposed Future Meetings 6
Free Workshops on Open-Source Tools for Chemistry 7
The COVID Moonshot 7
Practical Cheminformatics with Open-Source Software 11
The Catalyst Science and Discovery Centre Archives 12
Chemical Data Recovery 3: Legacy Chemical Data Recovery 15
Svante Wold, 1941-2022 22
Cheminformatics: a Digital History - Part 1 Early days at Sheffield: a Personal Perspective 23
Being #CompChemURG: Forging New pathways 28
UKeiG Call for Nominations for the Prestigious Tony Kent Strix Award 2022 29
Welcome to the New Era of Scientific Publishing 30
Greg Landrum Receives the Mike Lynch Award 37
Bioinformatics in the Post-AlphaFold 2 Era 38
Diana Leitch – Reflections on her Life in Chemistry, Chemical Information and Librarianship 45
Meeting Report: AI in Drug Discovery 50
AI4SD News 53
The IUPAC Green Book 55
RSC Historical Group – Women in Chemistry Symposium 56
ACS CINF Report for July 2022 57
News from CAS 57
Chemical Information / Cheminformatics and Related Books 59
Other Chemical Information News 61

We have already started compiling content for the winter newsletter, if you have suggestions or would like to contribute please get in touch.

 

The latest of the RSC CICAG workshops is now online https://youtu.be/Ka08REoGYvI.

Electrostatic effects along with volume restrictions play a major role in enzyme and receptor recognition. Evaluating electrostatic and shape similarities of pairs of molecules such as proposed versus known ligands can therefore be valuable indicators of prospective binding affinities. This workshop will demonstrate how to compute electrostatic and shape similarities using the open-source tool ESP-Sim github.com/hesther/espsim, doi.org/10.26434/chemrxiv-2021-sqvv9-v3. Available options for comparing electrostatics will be discussed interactively on selected examples of public datasets, along with advice on embedding and aligning molecules prior to computing similarities.

Whilst comparing molecules using 1D or 2D descriptors is well known, most molecules are three dimensional, as are biomolecule binding sites. The comparison of molecular shapes and electrostatics is particularly challenging and this workshop is a perfect introduction. Come along and you have a chance to ask questions directly.

All materials are available on GitHub https://github.com/hesther/espsim/tree/master/workshop

 

The latest version of iBabel is now available. The big change is iBabel is now a universal application.

More details here https://www.macinchem.org/ibabel/version5/ibabel5.php.

 

More details of the RSC CICAG meeting on Ultra-large Chemical Libraries are available.

This one-day meeting will be held on 10 August 2022 10:00-17:00, at Burlington House, London.

Registration is open https://www.rsc.org/events/detail/73675/ultra-large-chemical-libraries and a number of the speakers have been finalised and looks a great line-up.

Roger Sayle, NextMove Software Limited, United Kingdom
Carol Mulrooney, GSK, United States
Jan H Jensen, University of Copenhagen, Denmark
Noah Harrison, Evariste Technologies, United Kingdom
Peter Pogany, GSK, United Kingdom

There is still time to submit poster abstracts. A limited number of bursaries are available, the application form should be submitted to the organisers. A maximum of £300 will be reimbursed on submission of receipts.

If you would like to exhibit, sponsor or support this meeting please contact the organisers.

This meeting is supported by

 

The SCM team proudly announce our new AMS2022 release, with many new features and improvements.

New Parametrization ReaxFF & DFTB, reaction mapping, OLED tools

Full details are here

I also noted

We have also gotten reports of AMS2022 working correctly on the new Apple processors (M1), but we currently do not offer technical support for this platform.

 

I had a look at building combinatorial libraries using MOE on an MacBook Pro Apple M1 max.

Bottom line it is seriously fast.

Read more here...

 

The official release of GROMACS 2022 is now available.

• Free-energy kernels are accelerated using SIMD, which make free-energy calculations up to three times as fast when using GPUs
• A new formulation of the soft-cored non-bonded interactions for free-energy calculations allows for a finer control of the alchemical transformation pathways
• New transformation pull coordinate allows arbitrary mathematical transformations of one of more other pull coordinates
• New interface for multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) simulations with the CP2K quantum chemistry package, supporting periodic boundary conditions.
• grompp performance improvements
• Cool quotes music playlist
• Additional features were ported to modular simulator
• Added AMD GPU support with SYCL via hipSYCL
• More GPU offload features supported with SYCL (PME, GPU update).
• Improved parallelization with GPU-accelerated runs using CUDA and extended GPU direct communication to support multi-node simulation using CUDA-aware MPI.

If you are a Spotify user the Cool quotes music playlist may be of interest!

Note:

If you are running on Mac OS X, the best option is gcc. The Apple clang compiler provided by MacPorts will work, but does not support OpenMP, so will probably not provide best performance.

 

The latest Schrödinger Software Release 2022-1 brings support for Apple M1 machines in addition to a range of updates and new features.

Hit Identification & Virtual Screening

Pharmacophore Modeling

New alignmulticores.py script to align 3D ligands to a reference ligand with multiple disconnected cores [2022-1] Ligand Docking

Return SMARTS of the core used when running core constraint docking with MCS [2022-1] Input file that generated a Glide grid is saved in the grid archive to improve ease of making changes [2022-1]

Target Validation & Structure Enablement

Protein Preparation

Sped-up hydrogen atom assignment to be o(n) by system size [2022-1] Protein X-Ray Refinement

PHENIX/OPLS supports PHENIX 1.20 [2022-1] Multiple Sequence Viewer/Editor

Automatically save MSV projects [2022-1] Rapid selection of a subset of sequences based on user-defined percent identity or similarity relative to a reference sequence [2022-1] Improved ability to save one or more sequences by ‘right clicking’ to export [2022-1] Protein Homology Modeling

Selectively download only the PDB BLAST subset of the NR BLAST database for local homology modeling [2022-1] New Workflow Action Menu prompts for homology modeling enables single click access to structure quality assessment, reliability reports, additional loop refinement, and sidechain refinement and localized minimization [2022-1]

Platform Environment

Maestro Graphical Interface

Apple M1 Support [2022-1] New 2D Sketcher (beta) [2022-1] New Workflow Action Menus [2022-1] Antibody Modeling Homology Modeling [2022-1] Force Field

Improved accuracy of histidine parameters, particularly in FEP+ prediction of histidine pka’s [2022-1] Improved geometries for B-N bond containing compounds [2022-1] Up to 10x faster execution of FFBuilder when parameterizing hundreds of ligands through greater job distribution [2022-1] Workflows & Pipelining [KNIME Extensions]

New 2D Sketcher node [2022-1] Run from LiveDesign [2022-1]: Export to LiveDesign node can export all the structures so model results can be stored in new LiveReport(s) Model output columns can contain files (eg with pdf) Store an executed workflow in a LiveReport column

Medicinal Chemistry Design

Ligand Designer

Ability to specify a max number of enumerated compounds [2022-1] Added access to “Vendor ID” details in the Project Table for purchasable compounds [2022-1]

Lead Optimization

FEP+

FEP+ Correlation Plot [2022-1]: Display best fit line and equation of the line Modified reporting to show confidence intervals instead of standard deviations Web services [2022-1]: Improved performance when viewing map status Solubility FEP (Beta)

Access to trajectory, representative structures, FEP classifiers in the analysis tab [2022-1] Web Services will return fmp/fmpdb files instead of mae/csv for analysis [2022-1] AutoQSAR

DeepChemAutoQSAR now supports Windows and Mac platforms [2022-1] FPsim-GPU

New vendor column in similarity results [2022-1]

 

The pages comparing cheminformatics/compchem apps on the MacBook Pro M1max are proving very popular. Several readers have asked me to compare energy usage which is an excellent suggestion.

Based on a suggestion I purchased Nevsetpo Power Meter UK Plug Power Monitor Watts Meter Plug and I've used it to test a selection of tasks. Once plugged into a socket it monitors total energy consumption of anything device plugged in. Both machines were fully charged and the "Optimised battery charging" was switched off.

I tried a few computationally intensive tasks and details of energy consumption are here..

 

As some of you may have seen I've started the comparison of my new MacBook Pro Apple M1 max with my old Intel MacBook.

I'm slowly working through a variety of cheminformatics toolkits and computational chemistry applications, I'm trying to run some "real world" workflows so you can see what kind of performance improvement you might expect.

The index page is here https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php and I'll update it as a test more applications

When possible I've used the latest builds for the M1 arm architecture. Both machines were connected to power and had no other applications running. To date I've looked at the following.

• RDKit
• OpenBabel
• Jupyter
• SMINA
• Vortex
• MOE
• PyMOL

More to come.

 

A couple of new scripts have been added to the excellent MayaChemTools growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

RDKitFilterTorsionLibraryAlerts.py - Filter torsion library alerts Direct Link

And

Psi4CalculateInteractionEnergy.py - Calculate interaction energy Direct Link.

 

There have been a couple of new additions to the fabulous list of tools and scripts on MayaChemTools.

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

o Psi4GenerateConstrainedConformers.py http://www.mayachemtools.org/docs/scripts/html/Psi4GenerateConstrainedConformers.html>

o Psi4PerformConstrainedMinimization.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformConstrainedMinimization.html.

o Psi4PerformTorsionScan.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformTorsionScan.html.

These scripts rely on the presence of Psi4 https://psicode.org/ and RDKit in your environment. In addition, the script RDKitPerformTorsionScan.py http://www.mayachemtools.org/index.html for further details.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU LGPL as published by the Free Software Foundation.

 

This quarterly release includes:

• Intuitive enhancement of the protein preparation workflow and kinase conservation annotations for structure enablement
• Addition of filters to improve drug-likeness for medical chemistry design using Ligand Designer
• A new diversity approach to select compounds for Active Learning Glide workflows for hit discovery and lead optimization
• Greater control of custom R-group enumerations for hit discovery and lead optimization for multiple simultaneous substitutions

A detailed account of this release is available https://www.schrodinger.com/releases/new-features?

 

The confirmed speaker list for the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry meeting has been updated. This very popular meeting will be held as a virtual event (Monday-Tuesday, 27th-28th September 2021),

Keynote: AI for molecular design, past, present and future Ola Engkvist, AstraZeneca, SE

Keynote: Challenges and opportunities for machine learning in drug discovery Patrick Walters, Relay Therapeutics, US

PyPEF – an integrated framework for data-driven protein design and engineering Mehdi Davari, Leibniz Institute of Plant Biochemistry (IPB), DE

Exploring molecular space and accelerating drug discovery with MegaMolBART, a transformer-based generative model Michelle Gill, NVIDIA, US

Machine learning models for predicting human in vivo PK parameters using chemical structure and dose Olga Obrezanova, AstraZeneca, UK

Molecular transformer-aided biocatalysed synthesis planning Daniel Probst, IBM Research Europe, CH

Best practice for chemical language model de novo design of GPCR ligands: datasets, scoring functions and optimization algorithms Morgan Thomas, University of Cambridge, UK

‘Attending’ to co-crystals in the Cambridge Structural Datacenter Aikaterini Vriza, University of Liverpool, UK

Further details and registration can be found on the conference website https://www.maggichurchouseevents.co.uk/bmcs/AI_2021.htm.

 

ORCA is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties.

ORCA 5.0 is not just an update to the program. Even if much of the output will look very similar to previous versions, ORCA 5.0 is pretty much a completely new program. We have spent major efforts in redesigning and streamlining the core engine of the program. In fact, in designing the new engine, we have deeply re-thought the conceptual basis for quantum chemical program development for the next decades to come. The result is a program that is much leaner, much more efficient and much fitter for future extensions in an ever shifting hardware landscape. The full transition to our final vision of a modern quantum chemical program suite will likely be completed with ORCA 6, that we plan to release 2022. However, the improvements made in ORCA 5.0 are so numerous and so vast that we felt that now is the appropriate moment to share our work with the general public.

The link to the download is on the ORCA forum (requires registration) https://orcaforum.kofo.mpg.de/app.php/dlext/?cat=13.

 

The first 2021 release of the Amsterdam Modeling Suite, AMS2021.1, features many improvements and new functionality.

Automated reaction pathway searching
The new potential energy surface (PES) exploration tasks in the central AMS driver enable researchers to automatically discover transition states and local minima with any of our or external engines. Further improvements in the AMS driver Spherical wall potential (nanoreactors) D4 dispersion corrections also available for periodic systems (BAND, DFTB) force bias Monte Carlo available for all engines ForceField engine: performance optimization ForceField has been sped up by 2-3 orders of magnitude through a combination of improvements: MPI with force decomposition, particle mash Ewald, default non-bonded cutoff reduced to 15Å.

ParAMS: scripting toolbox for ReaxFF and DFTB parametrization
ParAMS was silently released last year. We are looking forward to your findings and suggestions when you test ParAMS to build your training data and optimize parameters.

ADF
Polarizable force field: QM/FQ Quantum Mechanics/Fluctuating Charges Unrelaxed dipole moment excited states Transition dipole moment between excited states POLTDDFT for fast excitation spectra: more fit sets for most elements r2SCAN-D4 XC functional (also for BAND) Eigenvalue-only self-consistent GW (evGW), New TZ3P and QZ6P basis sets for Many Body Perturbation Theory New Ligand-Field DFT(LFDFT) spectroscopy: ESR g-tensor doublets, XMCD

COSMO-RS
Improved handling of fluid thermodynamics with multiple species, e.g. different protonation and dissociation states, aggregation (with solvent), conformers (Graphical) User Interface improvements Package manager to (de)install additional components (COSMO-RS database, Quantum ESPRESSO, Machine Learning Potentials, Ligand-Field DFT) Option to output results into a spreadsheet Graceful interactive termination, also via GUI Improved UI to handle multiple molecules Sinkbox and Safebox for MD with molecule gun Support for PES exploration and other new features, and more…

Installation under MacOSX on YouTube https://youtu.be/BJe8iFoeUcg.

 

MayaChemTools is an ever increasing collection of python and perl scripts that support cheminformatics and computational chemistry.

The latest addition are based on PSI4 an open-source quantum chemistry package.

PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms. Several parts of the code feature shared-memory parallelization to run efficiently on multi-core machines. An advanced parser written in Python allows the user input to have a very simple style for routine computations, but it can also automate very complex tasks with ease.

The command line Python scripts based on Psi4 provide functionality for the following tasks:

• Calculation of single point energies
• Calculation of molecular properties and partial charges
• Performing structure minimization
• Generating molecular conformations
• Visualizing frontier molecular orbitals and dual descriptors
• Visualizing electrostatic potential on densities and molecular surfaces

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU LGPL as published by the Free Software Foundation.

 

The AMS2020.103 subrelease contains an important bug fix for analytic frequencies with PBE, see below for more details. Other improvements and bug fixes in COSMO-RS, AMSjobs, and other components are included in this subrelease as well, so we suggest updating to this subrelease.

The Amsterdam Modeling Suite provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.

Easy installation with downloadable binaries for Windows, Mac, and Linux. Graphical user interface to set up, run, monitor, visualize and analyze jobs. Run jobs on your laptop, desktop PC or a high-performance computing cluster. Python interface for advanced workflows, job management, and analysis

 

The video of the ChimeraX workshop is now online https://youtu.be/M2K72Kgk718.

The RSC CICAG YouTube channel is building up a very useful collection of videos https://www.youtube.com/c/RSCCICAG.

 

OpenChem is once again participating in the Google Summer of Code.

Avogadro 2 Project Ideas

• Project: Python-based Compute and Data Server
• Project: Biological Data Visualization
• Project: Scripting Bindings
• Project: Integrate with RDKit
• Project: Tools for Interactive Molecular Dynamics

Open Babel Project Ideas

• Project: Integrate CoordGen library
• Project: Implement MMTF format
• Project: Test Framework Overhaul
• Project: Develop a JavaScript version of Open Babel
• Project: Develop a validation and standardization filter

cclib Project Ideas

• Project: Support for QCSchema JSON output
• Project: Implement new parsers
• Project: Discovering computational chemistry content online

QC-Devs Project Ideas

• Project: Visualization of Molecular Structure and Reactivity
• Project: Extended Interoperability of ChemTools and Quantum Chemistry Software
• Project: Visualize Chemical Reactions
• Project: Extended interoperability of GOpt and Quantum Chemistry Software
• Project: Implement Workflows for Calculation and Usage of Databases of Isolated Atom Densities
• Project: Orthogonal Procrustes for Rectangular Matrices
• Project: Faster Molecular Integrals with Density-Fitting

3Dmol.js Project Ideas

• Project: Improve 3Dmol.js

gnina Project Ideas

• Project: Improve gnina

NWChem Project Ideas

• Project NWChem-JSON
• Project NWChem-Python-Jupyter Interface
• JSON-LD for Chemical Data

DeepChem Project Ideas

• Project: PyTorch Lightning Implementation
• Project: Semiconductor Modeling Support
• Project: Protein Language Models

Miscellaneous Project Ideas

• Project: OneMol: Google Docs & YouTube for Molecules

There are more details of the potential ideas here https://wiki.openchemistry.org/GSoCIdeas2021 or contribute your own idea.

 

Schrödinger have just announced the release of the latest update.

This release fully supports macOS 11, Big Sur, (with previous releases of the suite remaining unsupported on Big Sur).

Computers running ARM64-based processors such as the Apple M1 chip are unsupported.

 

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

DOI

Source code is on GitHub https://github.com/theochem/iodata, can be installed using conda or pip.

There is also OpenBabel, OpenBabel has support for 113 formats in total.

 

A really interesting update to Samson

SAMSON is a software platform for computational nanoscience. Its generic, open architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. The SAMSON application and the SAMSON SDK are developed by the OneAngstrom led by Stephane Redon. SAMSON stands for "Software for Adaptive Modeling and Simulation Of Nanosystems".

One of the most exciting features of SAMSON 2020 R3 is the introduction of cloud computing capabilities. In many design situations, a local computer might have too little processing power to perform advanced calculations (e.g. high-throughput screening, some molecular dynamics simulations, etc.). The latest update introduces the possibility to perform cloud calculations directly from SAMSON.

From the users’ point of view, this means it will now be possible to use some cloud-enabled SAMSON extensions to perform calculations in the cloud with a unified, integrated approach, and focus on science. An obvious immediate advantage is the access to raw computing power (based on existing and upcoming computing hardware), the possibility to run many jobs in parallel, compare numerical experiments, perform long calculations while still being able to use your desktop/laptop.

The full release note are here.

 

Just heard an update is available.

We are pleased to announce Schrödinger software release 2020-3, which is available for download now. This update includes usability improvements and performance enhancements across our entire suite of tools and features the first full release of Ligand Designer - an automated tool for medicinal chemists to quickly design and evaluate ideas - as well as a revamped Multiple Sequence Viewer that makes working with sequences easier than ever.

Full details here https://www.schrodinger.com/releases/new-features?.

Supports macOS 10.13 - 10.15.

 

A new version of MOPAC has been released full details are in this publication "A New Release of MOPAC Incorporating the INDO/S Semiempirical Model with CI Excited States" DOI.

We have incorporated the semiempirical INDO/S Hamiltonian into a new release of MOPAC2016, which has long been at the forefront of semiempirical quantum chemical methods (SEQMs). Our new code enables the calculation of excited states using the INDO/S Hamiltonian combined with a configuration interaction approach using single excitations (CIS), single and double excitations (CISD), or multiple reference determinants (MRCI) where reference determinants are generated using a complete active space (CAS) approach. The capacity to perform excited-state calculations beyond the CIS level makes INDO/CI one of the few low-cost computational methods capable of accurately modeling states with substantial double-excitation character. Solvent corrections to the ground-state and excited-state energies can be computed using the COSMO implicit solvent model, incorporating state-specific corrections to the excited states based on the solvent refractive index. We demonstrate that this code produces physically reasonable electronic structures, absorption spectra, and solvatochromic shifts at low computational costs for systems up to hundreds of atoms, and for both organic molecules and metal clusters.

The release notes are here.

And downloads here.

 

Independent Gradient Model Plot ( IGMPlot )

By using IGMPlot you can identify and quantify molecular interactions over a broad range: from non-covalent to covalent bonding, through metal coordination. This tool can be helpful for interpretation accessible to a wide community of chemists (organic, inorganic chemistry, including transition metal complexes and reaction mechanisms).

New Features:

• IBSI index: an Intrinsic Bond Strength Index (does not belong to the conventional class of bond orders like Mulliken or Mayer, or the Delocalization Index)
• BAF index: a Bond Asymmetry Factor
• WFX file format is now supported
• Development of a scoring function from promolecular electron density (possibility to probe noncovalent interfragment interactions or weak intramolecular interactions)
• Quantifying intramolecular pipi stacking at the QM level of theory
• Accelerated performances

The program is written in C++. IGMPlot has been installed and tested on several platforms: Linux, (computational center, laptop), MacOS, Windows10. It is a standalone program. Multi-core execution can be leveraged. In that case, the OpenMP programming interface must be installed prior to IGMPlot compilation for higher performances (optional).

The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

What's new compared to fpocket 2.0 (old sourceforge repo)

fpocket:

• is now able to consider explicit pockets when you want to calculate properties for a known binding site
• cli changed a bit
• pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas)
• druggability score has been reoptimized vs original paper. Yields now slightly better results than the original implementation.
• compiler bug on newer compilers fixed

mdpocket:

• can now read Gromacs XTC, netcdf and dcd trajectories
• can also read prmtop topologies
• if topology provided, interaction energy grids can be calculated for transient pockets and channels (experimental)

The GitHub page https://github.com/Discngine/fpocket contains detailed instructions for installation. This project is licensed under the MIT License

 

Just came across this site ConstruQt a molecular design tool that allows automated library-scale deployment of quantum chemical calculations.

• Transforms molecular drawings into accurate 3D structures and energies of conformational, tautomeric and stereoisomeric space
• Interactive visual navigation of the energies and structures
• Contribute to the worlds largest repository of relevant molecules for chemical research. Fully open to all.

They are also looking for feedback https://www.surveymonkey.com/r/5L9TMNX

 

This quarterly release includes usability improvements and performance enhancements across all of the software. Full release notes are here https://www.schrodinger.com/releases/new-features?.

 

xtb - An extended tight-binding semi-empirical program package can now be installed using conda

The extended tight binding program provides the geometry, frequency and non-covalent interaction (GFN) parametrisations of the tight binding Hamiltonians GFN1-xTB (JCTC 2017) and GFN2-xTB (JCTC 2019) and a preliminary version of the new GFN0-xTB https://doi.org/10.26434/chemrxiv.8326202.v1. All parametrisations consistently cover the entire periodic system up to Z=86 and include a continuum solvation model (GBSA) for common solvents.

conda install -c conda-forge xtb

Or

conda install -c conda-forge/label/cf202003 xtb

The user guide is available online https://xtb-docs.readthedocs.io/en/latest/contents.html and the source code is on GitHub https://github.com/grimme-lab/xtb/

dftd4 - A generally applicable London dispersion correction

This program implements the D4 London dispersion correction for molecular and 3D periodic systems. DOI and DOI.

conda install -c conda-forge dftd4

Or

conda install -c conda-forge/label/cf202003 dftd4

The source code is available on GitHub https://github.com/dftd4/dftd4 and includes build instructions and example usage.

To compile this version requires

• gfortran (8.2.1) or ifort (17.0.7 or 18.0.3) compiler
• meson (0.49.0) and ninja (1.8.2) as build system
• asciidoc (8.6.10) to build the man-page

 

The latest update to SAMSON 2020, the open molecular modelling platform is now available.

This update brings one feature that I'm many having been asking for.

• Molecular builder, you can build molecules by adding individual atoms or by adding Assets, an assets can be anything: rings, fragments, radicals, whole molecules, proteins, nanoparticles, 2D materials, etc.
• Tooltips, Hovering nodes now displays information about them and their ascendants.
• Tutorials, SAMSON now contains step-by-step Interactive tutorials that guide you through SAMSON’s features at your own pace.
• The SAMSON API has been upgraded to expose the new functionalities of this release and let developers create fantastic molecular modelling experiences that they can distribute on SAMSON Connect.

SAMSON itself is free, and so are many SAMSON Elements (extensions). For non-free extensions, it essentially works like Netflix. Monthly and yearly subscriptions are available, with lower prices for academia (typically 60% off). Users subscribe directly online at https://www.samson-connect.net. When they need group or site licenses, they contact us at sales@oneangstrom.com for quotes.

There are Elements for conformational analysis, docking, molecular dynamics, crystal creator, molecular optimisation, protein alignment and much more.

Create your own elements

It’s C++ and Qt for the interface there’s a tutorial to develop an app for example, and they actually put up slides about C++ as a refresher :-) here.

It's also possible to use python: https://documentation.samson-connect.net/scripting-guide/.

The core of SAMSON is not open source, but developers can do what they want with their modules (give their source or not), and the source of some of the modules are available on Github at https://github.com/SAMSON-Connect.

There is much more on Github https://github.com/1A-OneAngstrom/SAMSON-Developer-Tutorials.

 

OpenEye is pleased to announce the release of OpenEye Applications v2019.Nov

HIGHLIGHTS

• SPRUCE, a new application for preparing biomolecular structures for modeling applications, is now available in the OpenEye applications bundle.
• SZMAP now provides a simpler but enhanced workflow, using the newly released SPRUCE technology for structure preparation.
• SMIRNOFF, a small molecule force field from the Open Force Field Initiative, is now integrated into SZYBKI.

This is the last release to support macOS 10.12. Full support for macOS 10.15 will be added in the next release

 

DIRAC : Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations

The DIRAC program computes molecular properties using relativistic quantum chemical methods. It is named after P.A.M. Dirac, the father of relativistic electronic structure theory.

• EOMCC - core excitation and ionization energies via core-valence separation using projectors in RELCC (Avijit Shee, Andre Gomes, Marta Lopez Vidal). Manual: see keywords under "*CCPROJ"
• Python interface of DIRAC with Openfermion (Bruno Senjean) to perform relativistic quantum chemistry calculations simulated on a quantum computer .
• Nuclear Spin-Rotation tensors. Contributors: I. Agustin Aucar and Trond Saue. Reference: I. A. Aucar, S. S. Gómez, M. C. Ruiz de Azúa, and C. G. Giribet Theoretical study of the nuclear spin-molecular rotation coupling for relativistic electrons and non-relativistic nuclei.J. Chem. Phys. 136 (2012) 204119. Manual: ".SPIN-R" Tutorial: Nuclear spin-rotation constants.
• Nuclear Magnetic-Quadrupole-Moment interaction constant in KRCI (Malaya K. Nayak). Reference: T. Fleig, M. K. Nayak and M. G. Kozlov TaN, a molecular system for probing P,T-violating hadron physics.Phys. Rev. A 93 (2016) 012505

Mac/Unix install

DIRAC is configured using CMake , typically via the setup script, and subsequently compiled using make (or gmake). The setup script is a useful front-end to CMake.

 

An update to Amsterdam Modeling Suite (version 2019.3) has been released.

We thank all our external developers and collaborators across the globe for their ongoing support and efforts. Together we keep building on the user-friendly AMS platform, with the powerful compute engines tied together by the central AMS driver, the graphical interface, and a Python workflow environment. AMS2019.3 provides useful productivity enhancements for many applications and research projects.

Structure and Reactivity

• Microkinetics calculations from the GUI using Filot’s MKMCXX program
• Reaction path & TS search with CI-NEB with all engines
• Apply non-isotropic external stress to periodic systems
• Quick validation of transition states
• Energy decomposition analysis and ETS-NOCV with real unrestricted fragments

Molecular Dynamics

• Accelerate MD runs with Temperature Replica Exchange
• Non-equilibrium molecular dynamics (NEMD) for thermal conductivity
• New analysis tools: radial distribution functions, histograms, temperature profiles
• Faster visualization of trajectories for large systems

Faster Simulations

• Automatic double parallelization speeds up certain calculations by orders of magnitude
• Much faster periodic DFTB (including GFN1-xTB), analytic stress tensors
• Run calculations in the Amazon Web Services (AWS) cloud directly from ADFJobs
• Fast vibrationally resolved electronic spectra and resonance Raman

New Accurate Methods

• Double hybrid and MP2 energy calculations for molecules with hundreds of atoms
• Latest Grimme D4 dispersion corrections
• Implicit solvation model GBSA for molecular DFTB and GFN-xTB

New Interfaces

• New graphical user interface to VASP
• Python scripting with COSMO-RS
• Efficient pipe interface for AMS with external codes

The python scripting is pleasing to see, python is becoming the lingua franca and probably an essential component of any software package. There is more detail on the python support here.

The latest update works under Catalina. However there are still some minor issues (e.g. vtk bug on windows maximizing, these should be sorted soon).

 

A nice video showing the new/updated features in the latest release https://www.schrodinger.com/platform.

Not yet certified for Catalina.

 

I've done another update to the Fortran on a Mac page.

Added a number of open-source comp chem packages.

Many thanks to Sebastian Ehlert for highlighting dftd4.

 

Free energy perturbation (FEP) is a method that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations and used in a wide variety of applications.

FEP calculations have been used for studying host–guest binding energetics, pKa predictions, solvent effects on reactions, and enzymatic reactions. Other applications are the virtual Screening of ligands in drug Discovery, as well as for In silico mutagenesis studies. For the study of reactions it is often necessary to involve a quantum-mechanical (QM) representation of the reaction center because the molecular mechanics (MM) force fields used for FEP simulations can't handle breaking bonds.

In recent years this technique has gained popularity in predicting binding interactions in drug discovery, and it is great that Merck have made a benchmark dataset available on GitHub https://github.com/MCompChem/fep-benchmark. Details of which are described here DOI. Eight different targets are included together with 200 ligands.

CDK8, c-Met, Eg5, Hif2a, PFKFB3, SHP2, SYK, TNKS2

 

One of the highlights for me at the recent 2nd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry in Cambridge was the work of Adrian Roitberg and Olexandr Isayev et al on Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning DOI.

Here we train a general-purpose neural network potential (ANI- 1ccx) that approaches CCSD(T)/CBS accuracy on benchmarks for reaction thermochemistry, isomerization, and drug-like molecular torsions. This is achieved by training a network to DFT data then using transfer learning techniques to retrain on a dataset of gold standard QM calculations (CCSD(T)/CBS) that optimally spans chemical space. The resulting potential is broadly applicable to materials science, biology, and chemistry, and billions of times faster than CCSD(T)/CBS calculations.

The presentation was really compelling and really looks like an example where AI can be truly transformational. The good news is the code is all freely available on Github https://github.com/isayev/ASE_ANI, the bad news is that it "Works only under Ubuntu variants of Linux with a NVIDIA GPU" and Python binaries built for python 3.6 and CUDA 9.2.

In the past I would have stopped there but with the increasing number of external GPU and a NVIDIA CUDA Installation Guide for Mac OS X I'm wondering if there might be a path forward. I'd be very interested to hear about experiences with external GPU with NVIDIA graphics cards and using the CUDA toolkit on a Mac.

Update

Olexandr emailed me to to mention they have a pure Python version https://github.com/aiqm/torchani this will run on Mac however there is no GPU acceleration.

TorchANI is a pytorch implementation of ANI. It is currently under alpha release, which means, the API is not stable yet. If you find a bug of TorchANI, or have some feature request, feel free to open an issue on GitHub, or send us a pull requests

Also stumbled across the paper

Ab-Initio Solution of the Many-Electron Schrödinger Equation with Deep Neural Networks https://arxiv.org/abs/1909.02487Arxiv

 

An update to MOE has been released by Chemical Computing Group. This is a minor update but is recommended for all users.

However I'm sure this item will delight many users

Copy/Paste in popup menus. Copy and Paste menu items have been added to the MOE Popup menu. Copy menu items have been added to the various Entry and Field popups, including in the footer, of the Database Viewer.

 

ORCA is a general purpose quantum chemistry package that is free of charge for academic users. It has been developed since the late 90s and by now is one of the most heavily used quantum chemistry packages worldwide. It can be downloaded from the Website of the Max Planck Institut fuer Kohlenforschung at www.kofo.mpg.de

Commercial users should contact https://www.faccts.de/orca/

With a strong user base of more than 15.000 registered users in academia worldwide, ORCA is the fastest growing quantum-chemical software package to date.  ORCA provides cutting-edge methods in the fields of density functional theory as well as correlated wave-function based methods

ORCA 4.2 New Features

Local correlation

• Iterative (T) for open shells
• Multi-level scheme for open shell systems (all PNO accuracy levels)
• DLPNO-STEOM-CCSD for closed shells
• DLPNO-CCSD(T)-F12 for open shells
• Automatic fragmentation in LED analysis
• RIJCOSX-LED implementation
• HF-LD method for efficient dispersion energy calculations

Multi-Reference

• FIC-CASPT2 implementation including level shift and IP/EA shift.
• FIC-NEVPT2 unrelaxed densities and natural orbitals.
• CIPSI/ICE improvements. Can be run now with configurations, individual determinants or CSFs (experimental)
• FIC-ACPF/AQCC: variants of the FIC-MRCI ansatz
• Efficient linear response CASSCF
• Reduced memory requirements in MRCI and CIPSI/ICE

Spectroscopy

• GIAO EPR calculations (one issue with the SOMF operator still remaining)
• Improvements to ESD module for fluorescence, phosphorescence, bandshape, lifetime and resonance Raman calculations
• ESD now includes also the prediction of the Intersystem Crossing non-radiative rates
• Hyperfine couplings for CASSCF calculations (but not as response)

Excited states

• Spin-orbit coupling in TD-DFT
• MECP optimization for TD-DFT
• Conical Intersection Optimization
• Range-separated double-hybrids (B2PLYP, B2GPPLYP) for TDDFT
• Numerical and Hellmann-Feynman NACMEs using TD-DFT/CIS
• DLPNO-STEOM-CCSD for closed shells (also see 'Local correlation')

Solvation

• CPCM Gaussian Charge Scheme with the scaled-vdW surface and the Solvent Excluded Surface (SES). Available for single point energy calculations and geometry optimizations using the analytical gradient.

SCF/optimizer/semi-empirics/infrastructure etc.

• Nudge elastic band (NEB) transition states improvements (also works with xTB for initial path)
• Improved compound method scripting language for workflow improvements
• Improved ASCII property file
• Libxc interface allows a far wider range of density functionals to be used
• Interfaced with Grimmes GFN-xTB and GFN2-xTB
• Improvement of IRC algorithm
• Cartesian minimization (L-OPT) for systems with 100.000s of atoms, Minimization of specific elements (incl. H) only, fragment specific optimization treatment (relax all, relax hydrogens, rigid fragment, fixed fragments)

QM/MM and MM

• First release with ORCA-native MM and QM/MM implementation
• Automated conversion from NAMDs CHARMM format
• Automated generation of simple force-field for non-standard molecules
• Simple definition of active and QM regions
• Automated inclusion and placement of link-atoms
• Automated charge-shifts to prevent over-polarization
• MM and QM/MM work with all kinds of optimizations, NEB / NEB-TS methods, frequency analysis
• Option for rigid MM water (TIP3P) in MD simulation and optimization

Molecular Dynamics

• Added a Cartesian minimization command to the MD module, based on L-BFGS and simulated annealing. Works for large systems (> 10'000 atoms) and also with constraints. Offers a flag to only optimize hydrogen atom positions (for crystal structure refinement).
• The MD module can now write trajectories in DCD file format (in addition to the already implemented XYZ and PDB formats).
• The thermostat is now able to apply temperature ramps during simulation runs.
• Added more flexibility to region definition (can now add/remove atoms to/from existing regions).
• Added two new constraint types which keep centers of mass fixed or keep complete molecules rigid.
• Ability to store the GBW file every n-th step during MD runs (e.g. for plotting orbitals along the trajectory).
• Can now set limit for maximum displacement of any atom in a MD step, which can stabilize dynamics with poor initial structures. Runs can be cleanly aborted by "touch EXIT".
• Better handling/reporting of non-converged SCF during MD runs.
• Fixed an issue which slowed down molecular dynamics after many steps.
• Stefan Grimme's xTB method can now be used in the MD module, allowing fast simulations of large systems.

Miscellaneous

• Compute thermochemical corrections at different temperatures without recomputing the Hessian
• Fragments can now be defined in the geom block as simple lists
• Simpler input format for definition of atom lists and fragments, in particular useful for large atom lists
• basename.trj files are now called basename_trj.xyz

 

Sire is a free, open source, multiscale molecular simulation framework, written to allow computational modellers to quickly prototype and develop new algorithms for molecular simulation and molecular design. Sire is written as a collection of libraries, each of which contains self-contained and robust C++/Python building blocks. These building blocks are vectorised and thread-aware and can be streamed (saved/loaded) to and from a version-controlled and tagged binary format, thereby allowing them to be combined together easily to build custom multi-processor molecular simulation applications.

Sire is available via conda

conda install -c conda-forge -c omnia -c michellab sire

Note that on OS X you will need to run Python scripts with the sire_python interpreter. This is due to an issue with the default Python interpreter that is installed via Conda

You can also download the binary here

http://siremol.org/pages/binaries.html

And compile from source from GitHub

https://github.com/michellab/Sire

To compile Sire, you need a working C++ compiler with at least C++ 2014 support (gcc >= 5 or clang >= 3.7), cmake (version 3.0.0 or above), a Git client to download the source, and a working internet connection (needed by the Sire compilation scripts to download additional dependencies).

 

KiSThelP is a cross-platform free open-source program developed to estimate thermodynamic and kinetic properties from electronic structure data. To date, five computational chemistry software formats are supported (Gaussian, GAMESS, NWChem, ORCA, MOLPRO).

Some key features are:

• gas-phase molecular thermodynamic properties (offering hindered rotor treatment)
• thermal equilibrium constants
• transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart)
• RRKM rate constants, for elementary reactions with well-defined barriers.

For information, please visit: http://kisthelp.univ-reims.fr

 

The Open Force Field Consortium is an industry-funded effort to develop small molecule force fields.

0.4.1 - Bugfix Release This update fixes several toolkit bugs that have been reported by the community. Details of these bugfixes are provided here. It also refactors how ParameterType and ParameterHandler store their attributes, by introducing ParameterAttribute and IndexedParameterAttribute. These new attribute-handling classes provide a consistent backend which should simplify manipulation of parameters and implementation of new handlers.

 

The Open Force Field Initiative is an open source, open science, and open data approach to better force fields. All the code is on GitHib and they also provide highly curated datasets.

The idea is to enable molecular mechanics on small and macromolecules jointly using open and freely available software.

A recent blog post from Peter Schmidtke caught my eye.

Recently a few updates of the openforcefield toolkit came out … a game changer, as you’ll see.

The work investigated whether the 768 fragments from the XChem fragment library at Diamond can be parametrised with the new version of Open Force Field (0.4) and how they behave after a simple minimisation.

In short all fragments technically pass the parametrisation and minimisation step, this was supported by visual inspection.

All the code is on GitHub.

 

A recent publication "Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization" DOI caught my eye. Predicting ligand binding affinities is a very challenging process and whilst free energy perturbation methods have proved useful they are very computationally demanding. SILCS looks to give similar accuracy but with reduced computational demands.

The software is available from SILCSBIO and whilst it requires significant compute resources or access to a virtual cluster using Amazon Web Services, the SilcsBio Graphical User Interface (GUI) enables running SILCS and SSFEP simulations and analysing results through a GUI instead of the command line and is available for Mac OSX and Windows. Visualisation of results uses VMD or PYMOL plugins.

 

The Amsterdam Modeling Suite 2019 (AMS2019) has been released.

Full details and release notes are here

Full documentation https://www.scm.com/doc/Documentation/index.html

Download binaries here https://www.scm.com/support/downloads/.

 

This may be of interest Special Issue on Emerging Architectures in Computational Chemistry

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

OpenMP in VASP: Threading and SIMD

Field‐programmable gate arrays and quantum Monte Carlo: Power efficient coprocessing for scalable high‐performance computing

Coupled‐cluster singles, doubles and perturbative triples with density fitting approximation for massively parallel heterogeneous platforms

Domain‐specific virtual processors as a portable programming and execution model for parallel computational workloads on modern heterogeneous high‐performance computing architectures

 

I'm sure many will have noticed the release of Mathematica version 12, the website contains details of the many additional new features, but I happened to notice there were a couple of Chemistry features including:

• MoleculePlot https://reference.wolfram.com/language/ref/MoleculePlot.html for creating 2D plots of molecules and highlighting features like bonds or atoms.

  m = Molecule["O=C(C1CCC1)S[C@@H]1CCC1(C)C"];
MoleculePlot[m, {Bond[{"C", "O"}, "Double"], Atom["C", "RingMemberQ" -> True]}]

  

• MoleculePlot3D https://reference.wolfram.com/language/ref/MoleculePlot3D.html creates a three-dimensional model of the molecule.

The Molecule is a symbolic representation of a chemical species and is a fully computable first-class member of the Wolfram Language. More details here.

 

The 0.2.0 release of the Open Force Field Toolkit, featuring RDKit support and the new-and-improved SMIRNOFF v0.2 force field spec has been announced. https://openforcefield.org/news/openforcefield-toolkit-0.2-release/.

We're excited to announce the public release of the Open Force Field toolkit version 0.2.0! Most notably, this release adds the ability to assign SMIRNOFF parameters and AM1-BCC charges with a completely open-source backend, adding support for the RDKit and AmberTools via a new ToolkitWrapper infrastructure that can be extended in the future to support additional cheminformatics toolkits. The OpenEye Toolkit will continue to be supported, as well as used internally our parameter-fitting pipelines in the short term. We're extremely grateful to the long list of contributors that have made this release possible, especially Shuzhe Wang from the Riniker group for piloting much of the RDKit functionality.

 

Just saw an interesting paper "QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics" DOI.

QUBEKit is python based force field derivation toolkit that allows users to derive accurate molecular mechanics parameters directly from quantum mechanical calculations.

Code is available on GitHub QUBEKit, and there is a user tutorial on the Wiki Page.

Requirements:

• Anaconda3
• Biochemical and Organic Simulation System (BOSS)
• OpenMM
• Gaussian09
• ONETEP
• Matlab 2017

Python modules used:

• numpy
• argparse
• collections
• colorama
• matplotlib

 

Just got this notice.

We are pleased to announce Py-ChemShell 2019 (v19.0), the first beta release of the Python-based version of ChemShell. Py-ChemShell 2019 offers new interfaces to ORCA and DL_POLY 4, a complete task-farmed parallelisation framework (including parallel finite difference gradients), RESP charge fitting procedures, and case studies for problems in materials modelling.

Py-ChemShell can be downloaded free of charge under the open source GNU LGPL v3 licence from this site.

ChemShell is a scriptable computational chemistry environment for multiscale modelling. While it supports standard quantum chemical or force field calculations, its main strength lies in hybrid QM/MM calculations. The concept is to leave the time-consuming energy evaluation to external specialised codes, while ChemShell takes over the communication and data handling.

ChemShell provides interfaces to a variety of QM and MM codes, including:

• GAMESS-UK
• NWChem
• FHI-aims
• DALTON
• MNDO
• TURBOMOLE
• Orca
• Molpro
• Gaussian
• DMol3
• Q-Chem
• DL_POLY
• GULP
• CHARMM
• GROMOS

 

The 2019.01 release of Chemical Computing Group's Molecular Operating Environment software includes a variety of new features, enhancements

Full release notes are here.

includes:

• Calculate and Analyze pH-Dependent Protein Properties
• MOEsaic Session Sharing and Project Customization
• Determine Conformation Population from NMR NOE Data
• Predict Relative Binding Energies with AMBER Thermodynamic Integration

Worth noting there is an updated Version of Flexera License Manager.

MOE now uses an updated version of the Flexera license manager. The license manager server components lmgrd, chemcompd, and lmutil have all been updated to version 11.16.0.0. Note that older versions of MOE will continue to run with updated license manager servers.

 

An update to LICHEM: Layered Interacting CHEmical Models has been published DOI

LICHEM is an open-source (GPLv3) interface between QM and MM software so that QM/MM calculations can be performed with polarizable and frozen electron density force fields. Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations.

Available from GitHub https://github.com/CisnerosResearch/LICHEM.

Note, On OSX machines, the SEDI, TEX, BIB, and CXXFLAGS variables will need to be modified.

 

With the release of ORCA 4.1, they have moved our forum and download site to a new server at the Max Planck Institute fuer Kohlenforschung, where the ORCA team now has its home base. Now at https://orcaforum.kofo.mpg.de.

ORCAis an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. DOI.

List of new features for ORCA 4.1:

SCF/DFT

• B97M-V, wB97M-V, wB97X-V plus various D3 variants of B97 functionals
• Simple input keywords for DSD-BLYP, DSD-PBEP86, and DSD-PBEB95
• CPCM analytic Hessian
• DLPNO-double hybrid DFT including gradient
• SymRelax option in %method

Semiempirical methods

• XTB method of Grimme et al.

Coupled cluster

• Iterative solution of the full (T) equations for DLPNO-CCSD(T)
• Open shell DLPNO-CCSD density and spin density matrices
• Full DLPNO-MP2 gradient
• CIM (Cluster in molecules) Implementation with MP2, CCSD(T), DLPNO-MP2 and DLPNO-CCSD(T)
• IP and EA coupled cluster methods and their DLPNO variants
• STEOM-CCSD for open shells
• SOC between bt-PNO-STEOM and STEOM states
• Improved Multilevel implementation including multilevel DLPNO-IP
• F12-Triples scaling for RHF canonical CCSD(T) based on the CCSD/ CCSD-F12 ratio

Multireference

• New CASSCF SuperCIPT converger is reliable and efficient.
• New options for final orbitals to find partner orbitals for the chosen active space e.g. bonding / anti-bonding partners.
• MC-RPA (Multiconfigurational random phase approximation)
• ◦ AO driven integral direct for calculations on larger molecules
• ◦ Fock matrix -> conventional, direct, RIJ/COSX
• ◦ MPI parallel
• ◦ NTOs for visualizing transitions
• Checking stability of state specific CASSCF wave functions by orca_mcrpa
• Dynamic correlation dressed (DCD-CAS) method with inclusion of relativistic effects (SOC, spin-spin, magnetic fields)
• CASSCF RIJCOSX allows two separate auxiliary basis sets
• CASCI/NEVPT2 protocol for XAS and RIXS

Optimization

• Nudge elastic band method to locate transition states
• Enabled 3-dimensional relaxed potential energy surface scan
• Improvement of redundandant internal coordinate generation
• Faster and more smooth convergence for 3-dimensional systems and embedded cluster models
• Intrinsic reaction coordinate (IRC) following
• Swart model Hessian (good for weak interactions)

Molecular Dynamics

• MD simulations can now use Cartesian, distance, angle, and dihedral angle constraints.
• The MD module now features cells of several geometries (cube, orthorhombic, parallelepiped, sphere, ellipsoid), which can help to keep the system inside of a well-defined volume.
• The cells can be defined as elastic, such that their size adapts to the system. This enables to run simulations under constant pressure.
• Ability to define regions (subsets of atoms) enables applications such as thermostating different parts of the system to different temperatures (cold solute in hot solvent, temperature gradients, ...)
• Trajectories can now be written in XYZ and PDF file format.
• A restart file is written in every simulation step. Simulations can be restarted to seamlessly continue.
• The energy drift of the simulation is now displayed in every step.
• The MD module now works with a broader range of methods (semiempirics, ECPs, QM/MM).
• Fixed a bug in the time integration of the equations of motion which compromised energy conservation.

Spectroscopic properties

• orca_pnmr module tool to calculate paramagnetic NMR spectra
• NMR chemical shifts with RI-MP2 and double hybrid DFT including GIAO’s, spin-component scaling and CPCM
• NMR Spin-Spin coupling in calculations with DFT/HF
• NMR wth ZORA
• Maximoff-Scuseria correction for the kinetic energy density in GIAO-based calculations with meta-GGA functionals
• Exact and gauge invariant transition moments and approximate decomposition into dipole, quadrupole etc terms in all modules.
• PNO-ROCIS method for more efficient X-ray absorption calculations
• IP-ROCISD for high spin ROHF references
• TD-DFT:
• Transient spectra (excited state absorption) for CIS/TDA
• Triplet gradients (with RIJ, COSX and all) for all cases.
• Spin orbit coupling (including CPCM) and gradients
• Root following scheme for optimization
• Slow term to correct energy of relaxed excited state
• Full TD-DFT with double hybrids
• ESD module to calculate spectroscopic properties
• Vibrationally resolved absorption spectra including Duschinsky rotation and/or vibronic coupling.
• Fluorescence and Phosphorescence rates with same options.
• Resonance Raman spectra with the same options
• works with CIS/TDDFT, ROCIS, CASSCF and EOM/STEOM.
• Seven different schemes for obtaining an excited state PES and five different choices of coordinate systems

Analysis tools:

• Open Shell LED
• Dispersion interaction Density plots
• LED for DLPNO-MP2
• LED for the frozen state
• Update of AIM interface
• NBO 7 compatibility (i4)
• Miscellaneous
• Compound method (Infrastructure, plus W2.2, W1, G2(MP2), G2(MP2-SVP), G2(MP2-SV) methods)
• Property file (additional properties, plus new infrastructure)
• Decomposition of correlation energy for canonical RHF CCSD energies to singlet - triple pairs
• Additional EP2 extrapolation schemes using RI-MP2 and DLPNO-MP2 methods as cheap methods (request from forum)
• Lanthanide new def2 basis sets
• def2-XVP/C auxiliary basis sets for Ce-Lu by Chmela and Harding.
• Robust Second order optimizer for localized orbitals
• Added a few basis sets.

 

The DIRAC program computes molecular properties using relativistic quantum chemical methods. It is named after P.A.M. Dirac, the father of relativistic electronic structure theory.

I can be downloaded from the zenodo repository.

New features are described here.

DIRAC, a relativistic ab initio electronic structure program, Release DIRAC18 (2018), written by T. Saue, L. Visscher, H. J. Aa. Jensen, and R. Bast, with contributions from V. Bakken, K. G. Dyall, S. Dubillard, U. Ekström, E. Eliav, T. Enevoldsen, E. Faßhauer, T. Fleig, O. Fossgaard, A. S. P. Gomes, E. D. Hedegård, T. Helgaker, J. Henriksson, M. Iliaš, Ch. R. Jacob, S. Knecht, S. Komorovský, O. Kullie, J. K. Lærdahl, C. V. Larsen, Y. S. Lee, H. S. Nataraj, M. K. Nayak, P. Norman, G. Olejniczak, J. Olsen, J. M. H. Olsen, Y. C. Park, J. K. Pedersen, M. Pernpointner, R. Di Remigio, K. Ruud, P. Sałek, B. Schimmelpfennig, A. Shee, J. Sikkema, A. J. Thorvaldsen, J. Thyssen, J. van Stralen, S. Villaume, O. Visser, T. Winther, and S. Yamamoto (available at https://doi.org/10.5281/zenodo.2253986, see also http://www.diracprogram.org).

 

A recent publication described OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Feature DOI.

We present Osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of osprey when running the same algorithms on the same hardware. Moreover, osprey 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of osprey, osprey 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Finally, we show here empirically that osprey 3.0 accurately predicts the effect of mutations on protein–protein binding.

Osprey 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open‐source software GPLv2.

The source code is available on GitHub https://github.com/donaldlab/OSPREY3/.

Unfortunately the installation instructions do not include Mac OSX but there are instructions for "Debian-like Linux" which seemed promising. With the invaluable help of Nathan Guerin I was able to get OSPREY installed.

Read more…..

 

Just got details of an interesting service

ChemAlive (www.chemalive.com) would like to offer ConstruQt, its core molecular design tool based on quantum mechanics (QM), for trial.

Currently you can:

• Transforms list of SMILES or InChI molecular designations into state-of-the-art 3D molecular structures in SD format
• Manages the conformational space of the molecules with a robust shape searching algorithm
• Generates all reasonable tautomeric forms of the molecule and prioritizes them by energy
• Generates all diastereomeric forms of the molecules and differentiates them by energy
• All molecules are stored in our unique database architecture making the calculations easily augmented and carried through to other processes

The last bullet point is worth noting, so don't submit anything confidential.

 

The new IGMPlot release 2.4, is available for download at http://igmplot.univ-reims.fr . It provides chemists with a visual analysis of covalent and non-covalent interactions

Detailed installation notes are in the documentation (page 5).

IGMPlot is written in C++. It has been installed and tested on several platforms: computational centers (linux), MacOS, Windows10, and several compilers and versions (GNU, Intel, PGI), it can be compiled with or without OpenMP support

On MacOs machines, a sequential version of IGMPlot can be obtained with the Clang compiler. In the Makefile choose the options:

• CppCompilerFamily=GNU
• CppCompilerVersion=5andabove o OpenMP=NO
• CC=g++

On MacOS machines, to leverage OpenMP multicore execution, you must install a gcc (g++) version different from the one provided within the compiler front end “Clang” which until now has not built-in support for OpenMP. You might install gcc with the command: ‘brew install gcc -- without-multilib’ (see for instance https://stackoverflow.com/questions/35134681/installing- openmp-on-mac-os-x-10-11). This way, the compiler might be installed somewhere like /usr/local/Cellar/gcc/7.1.0/bin/g++-7. In this example, make sure the g++-7 command be available with your PATH and adjust the IGMPlot makefile accordingly (changing the g++ command with g++-7 for instance).

This link might also be useful OpenMP under MacOSX.

 

Now on GitHub https://github.com/MobleyLab/SAMPL6.

SAMPL6 Part II will include a octanol-water log P prediction challenge and will be followed by a joint D3R/SAMPL workshop in San Diego, Aug 22-23, 2019, immediately before the San Diego ACS National Meeting. A special issue or special section of JCAMD will be organized to disseminate the results of this challenge.

 

The Open Force Field Consortium, an academic-industry collaboration designed to improve small molecule force fields used to guide pharmaceutical drug discovery.

The Consortium will develop an extensible, open source toolkit for constructing, applying, and evaluating force fields; produce and curate public datasets necessary to build high-accuracy biomolecular force fields; and apply these tools and datasets to generate improved force fields. Academic and industry partners work together to ensure its success.

 

There is a new Turbomole release

TURBOMOLE has been developed to provide a fast and stable code to treat molecules for industrial application. With the TUBROMOLE implementation of RI-DFT, one of the fastest DFT methods will be available at your fingertips.

TURBOMOLE V7.3 (July 2018) New features:

• PNO-CCSD(T0) and PNO-CCSD(T) energies for closed-shell systems [1]
• new DFT-D4 dispersion correction based on xTB [2]
• modernized NMR (with RI-J, COSMO, meta-GGAs, low-order scaling HF-exchange, SMP parallelization) [3]
• VCD spectra using COSMO
• periodic DFT with larger basis sets (treatment of linear dependency)
• two-photon absorption cross sections and analytic frequency-dependent hyperpolarizabilities with TDDFT/TDHF [4]
• X2C gradients for 1- and 2-component DFT, full X2C and DLU-X2C [5]
• vibronic absorption/emission spectra (new module: radless) [6]
• CC2 vertical excited states with COSMO [7]
• NTO (natural transition orbitals) for TDDFT
• RI-GW based on dRPA (very fast GW and BSE) [8]

Efficiency:

• GW and Bethe-Salpeter based on fast dRPA
• support of RI-J and linear scaling HF exchange in NMR calculations
• PNO-MP2 closed shell energy calculations significantly more efficient

Usability:

• new scripts for parallel execution which recognize the most frequently used queuing systems

TmoleX (4.4) now supports:

• PNO-MP2, PNO-CCSD, PNO-CCSD(T0) and PNO-CCSD(T)
• DFT-D4 dispersion correction
• X2C relativistic two-component treatment for spin-orbit coupling terms, and new X2C basis sets
• Fukui indices and functions (calculation and visualization)
• movie exports to mp4 file format
• B97-3c functional

 

OpenEye have just announced the release of OMEGA v3.0.1 This upgrade fixes several bugs and adds a number of internal improvements.

Major bug fixes

• A bug that caused memory leaks in OMEGA classic, dense, pose, and rocs modes, has been fixed. Previously, a substantial memory leak was experienced when running OMEGA on a large database.
• OMEGA macrocycle no longer uses excessive memory for molecules with terminal heavy atoms.

OMEGA performs rapid conformational expansion of drug-like molecules, yielding a throughput of tens of thousands of compounds per day per processor. OMEGA is very effective at reproducing bioactive conformations, and provides an optimal balance between speed and performance when used on large compound databases.

 

Nominations are now open for the Computers in Chemistry division of the ACS awards.

More details here http://www.acscomp.org/awards.

 

Schrödinger have announced a major update their software suite.

Full details are here https://www.schrodinger.com/newfeatures

 

BioSolveIT have announced significant changes and improvements in SeeSAR resulting in another major release to version 8. The biggest change is that they now provide full protein visualization support. While the focus of the tool is for the most part still on the defined binding site, you can now...: see the whole protein in all its glory! As always, a major update means that HYDE scores must be re-calculated to stay in line with the changes made in the underlying structures. We certainly believe that these enhancements are well worth it:

• improved alignment
• full protein support in the seqence view
• search&find specific amino acids, waters or other protein components
• all protein visualization controls bundled
• enhanced pharmacophore handling
• fragment growing for covalent binders

For details see: https://www.biosolveit.de/SeeSAR/changes.html

They also have two new tools:

REALSpaceNavigator is the world's largest, ultra-fast searchable chemical space developed in collaboration with Enamine Ltd. It comprises roughly 3.8 billion compounds today, which will be delivered on demand in less than 4 weeks with an exceptional success rate of 80% and above.

PepSee is a software tool for interactive, visual compound prioritization as well as the design of next-generation peptide therapeutics. Peptide design ideally supports a multi-parameter optimization to maximize the likelihood of success. PepSee visualizes the relevant parameters at hand, side by side with the sequence data. Color-coded display stimulates SAR exploration. The main features of PepSee comprise:

• comfortable sequence & data import (from Excel, FASTA, PLN, Text, even PDF)
• automated as well as manual sequence alignment
• various data coloring and plotting options
• organizing and annotating your compounds
• interactive design of novel peptides

 

The new RSC CICAG website is now live http://www.rsccicag.org why not have a look and provide suggestions and feedback.

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community.

Also provides links to the social media feeds (Twitter, LinkedIn etc.)

 

deMon (density of Montréal) is a software package for density functional theory (DFT) calculations. It uses the linear combination of Gaussian-type orbital (LCGTO) approach for the self-consistent solution of the Kohn-Sham (KS) DFT equations. The calculation of the four-center electron repulsion integrals is avoided by introducing an auxiliary function basis for the variational fitting of the Coulomb potential.

The user guide provides installation instructions and requires a Fortran compiler, BASH and MPI.

 

Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active develpment community

Amber 18 ajor new features include:

• Free energy calculations on GPUs
• GPU support for 12-6-4 ion potentials
• Domain decomposition for CPU-parallelism
• Nudged elastic band calculations for pmemd (CPU and partial GPU implementation)
• Constant redox potential calculations, to supplement constant pH simulations
• Support and significant performance improvements for the latest Maxwell, Pascal and Volta GPUs from NVIDIA.
• New pmemd.gem code for advanced force fields, including AMOEB

AmberTools 18 new features include

• CUDA-enabled pbsa solver; extensions for membrane modeling with PB *lambda-dynamics method for constant pH simulations *packmol_memgen tool for building lipids and bilayers *New ("middle") integration algorithms in sander *Build tools based on CMake *Continued updates and extensions to cpptraj: *ability to obtain energies from snapshots of PME simulations *Pairlist and other speedups *improved scripting abilities

Instructions for installing Amber under Mac OSX are here http://ambermd.org/Installation.php

You will need to install gfortran, whilst you can download the binary it might be worth considering using Homebrew as described here

 

Just catching up.

NWChem 6.8 is now available on Github https://github.com/nwchemgit/nwchem.

NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of force fields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

Instructions for compiling NWChem on various platforms including Mac OSX https://github.com/nwchemgit/nwchem/wiki/Compiling-NWChem.

 

SAMSON has been updated with a number of cool features, I particularly like the embedded Jupyter console.

SAMSON is a platform for computational nanoscience.

Python scripting is now available! Most of the SAMSON API is exposed in Python, and a Jupyter console embedded in SAMSON allows you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.

What’s more, Python makes it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few.

 

The latest update to Chemical Computing Group's Molecular Operating Environment (MOE) software includes a variety of new features, enhancements

Windows XP (finally!) and macOS 10.6 have been removed from the list of officially supported platforms. Supported Windows platforms are Vista/7/8/10, and the minimum supported macOS is 10.7 (Lion).

Amber14:EHT Forcefield. The Amber14 parameter set is now supported in MOE. The new parameters consist of improvements to nucleic acids; otherwise, protein and small molecule parameters (and charges) are unchanged. The forcefield can be selected in the MOE | Footer.

TCR-MHC Protein Complex Database. A new MOE Project database containing T-Cell Receptor (TCR) – Major Histocompatibility Complex (MHC) x-ray structures has been added to MOE. The database can be accessed with MOE | Protein | Search | TCR-MHC | TCR-MHC which will launch the MOE Project Search panel.

Several applications have been parallelized to run in the moe -mpu environment:

• Descriptor calculations with the SVL function QuaSAR_DescriptorMDB.
• Energy minimization in the Database Viewer DBV | Compute | Molecule | Energy Minimize.
• Conformational search using MDB input files in MOE | Compute | Conformations | Search.
• Rotamer library generation with DBV | Compute | Build Rotamer Library.
• Project database creation with the SVL run file dbupdate.svl and the scripts $MOE/bin/projupdate and $MOE/bin/projupdate.bat.

I plan to review the latest version of MOE in the near future.

 

An interesting publication in JCIM, Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules, DOI.

We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios.

 

YANK is a GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

Features

• Modular Python framework to facilitate development and testing of new algorithms
• GPU-accelerated via the OpenMM toolkit
• Alchemical free energy calculations in both explicit and implicit solvent
• Hamiltonian exchange among alchemical intermediates with Gibbs sampling framework
• General Markov chain Monte Carlo framework for exploring enhanced sampling methods
• Built-in equilibration detection and convergence diagnostics
• Support for AMBER prmtop/inpcrd files
• Support for absolute binding free energy calculations
• Support for transfer free energies (such as hydration or partition free energies)

Install using conda

$ conda config --add channels omnia --add channels conda-forge
$ conda install yank

conda will install dependencies from binary packages automatically, including difficult-to-install packages such as OpenMM, numpy, and scipy. YANK runs on Python 3.5, and Python 3.6

 

Python seems to becoming the lingua franca for scientific scripting/progamming and it is perhaps not surprising that we now see increasing support for computational chemistry.

Chemtools is a set of modules that is intended to help with more advanced computations using common electronic structure methods/ programs. Currently the is some limited support for Gamess-US and MolPro program packages but other codes can be easily interfaced. It requires:

• Python works with Python 2.7.x and 3.x
• numba
• numpy
• mendeleev
• scipy
• setuptools

Chemtools is NOT hosted on pypi yet but in can be installed by pip from the bibbucket repository with:

pip install https://bitbucket.org/lukaszmentel/chemtools/get/tip.tar.gz

Pygamess is a GAMESS wrapper for Python, it requires:

• Python 2.6 or later (not support 3.x)
• RDKit
• GAMESS

It can be installed using pip

pip install pygamess

Usage

single point calculation with RDKit

from pygamess import Gamess
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("CC")
m = Chem.AddHs(m)
AllChem.EmbedMolecule(m)
0
AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
g = Gamess()
nm = g.run(m)
nm.GetProp("total_energy")
'-78.302511990200003'

PyQuante: Python Quantum Chemistry, an open-source suite of programs for developing quantum chemistry methods, it currently supports

• Hartree-Fock: Restricted closed-shell HF and unrestricted open-shell HF;
• DFT: LDA (SVWN, Xalpha) and GGA (BLYP) functionals;
• Optimized-effective potential DFT;
• Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques; C and Python interfaces to all of these programs;
• MINDO/3 semiempirical energies and forces;
• CI-Singles excited states;
• DIIS convergence acceleration;
• Second-order Moller-Plesset (MP2) perturbation theory.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically

• ADF (versions 2007 and 2013)
• DALTON (versions 2013 and 2015)
• Firefly, formerly known as PC GAMESS (version 8.0)
• GAMESS (US) (version 2012)
• GAMESS-UK (version 7.0)
• Gaussian (versions 03 and 09)
• Jaguar (versions 7.0 and 8.3)
• Molpro (versions 2006 and 2012)
• NWChem (versions 6.0 and 6.5)
• ORCA (versions 2.9 and 3.0)
• Psi (versions 3.4 and 4.0)
• Q-Chem (version 4.2)

FragBuilder a tool to create, setup and analyse QM calculations on peptides. DOI.

Update

And of course there is OpenBabel that can be used create input files for a variety of computational chemistry packages.

If I've missed anything please feel free to let me know.

 

LigParGen is a web-based service that provides force field (FF) parameters for organic molecules or ligands, offered by the Jorgensen group.

It is available here. http://zarbi.chem.yale.edu/ligpargen/

LigParGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14CM1A or 1.14CM1A-LBCC partial atomic charges. Server provides parameter and topology files for commonly used molecular dynamics and Monte Carlo packages OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO. Also, the PQR file is generated. Supported input formats: SMILES, MOL and PDB.Maximum ligand size allowed is 200 atoms.

It is also possible to install LigParGen locally on Mac or Linux machines using Anaconda as described here

More details here

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands, DOI

 

A little while back I mentioned BioConda. You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", DOI. Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. Looking through the packages it is clear there it already contains a number of chemistry packages. These include: Updated 24 November 2017

• OpenBabel
• Rdkit
• Opsin
• chemfp
• gromacs
• osra
• Autodock Vina
• openmg
• align-it
• strip-it
• shape-it
• np-likeness-scorer
• PubChem.py
• Smina

Bioconda offers a collection of over 3100 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 330 contributors. Rather than try to duplicate this effort for a "Chemconda" it seems more efficient to encourage chemists to contribute to Bioconda. If you do package a chemistry application for Bioconda please let me know and I'll publicise it on my blog and add it to the list above. To start things rolling I've added PubChem.py to Bioconda and I've written a page describing how to create a bioconda recipe.

Link to page Creating a Bioconda recipe

 

The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. The code is freely available under the GNU LGPL license.

It requires

• Python 2.7, 3.4-3.6
• NumPy

Optional:

• SciPy
• For ase.gui: Matplotlib (2D Plotting)

It can be installed using PIP

pip install --upgrade --user ase

Full details of the MacOSX installation are here.

 

Version 1.3: Add pKa prediction challenge instructions, input files, submission template files, update on the future plans of logD challenge.

SAMPL6 pKa Challenge Instructions

Challenge timeframe: Oct 25, 2017 to Jan 10, 2018

This challenge consists of predicting microscopic and macroscopic acid dissociation constants(pKa)s of 24 small organic molecules. These fragment-like small molecules are selected for their similarity to kinase inhibitors and for experimental tractability. Our aim is to evaluate how well current pKa prediction methods perform with drug fragment-like molecules through blind predictions.

Three formats of pKa prediction results will be evaluated:

• microscopic pKa values and related microstates
• microstate populations as a function of pH
• macroscopic pKa values

 

SAMPL6 includes challenges based on aqueous host-guest binding data (binding free energies and, optionally, binding enthalpies) for three different host molecules; and on physical properties (distribution coefficients and possibly solubilities), for a set of fragment-like molecules. The host-guest systems are useful to test simulation methods, force fields, and solvent models, in the context of binding, without posing the setup issues and computational burden of protein simulations. The physical properties offer efficient tests of force field accuracy when detailed simulations are used, and can also test pKa prediction methods, continuum solvation models, and knowledge-based prediction methods. SAMPL6 will also introduce a new challenge component, the “SAMPLing challenge”, in which computational methods will be evaluated on how efficiently their calculations approach well-converged reference results generated by the organizers. Participants will be provided with machine readable setup files for the molecular systems, including force field setups, along with recommended cutoffs and treatments of long-ranged interactions. The SAMPLing challenge is expected to include one or more cases from each challenge component (host-guest binding on each system; log D calculation).

If you would like to participate in the challenge join up here.

 

An interesting development for those working in nano materials.

We have completed the development of IM-UFF (Interactive Modeling - UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physically-based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience.

This contribution has been submitted to the Journal of Molecular Modeling.

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON’s generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means “Software for Adaptive Modeling and Simulation Of Nanosystems”.

 

I've written a couple of docking/virtual screening workflows using SMINA, a freely available tool DOI. There are a number of other alternatives and it is very difficult to get good comparisons which is why the Grand Challenges are useful.

The Grand Challenge 3 (GC3) is a blinded prediction challenge for the computational chemistry community, with components addressing pose-prediction, affinity ranking, and free energy calculations. GC3 is based on six different protein targets, Cathepsin S and five different kinases, and is separated into five subchallenges, some of which involve multiple protein targets. Only Cathepsin S is associated with cocrystal structures, so the kinase components of this challenge focus on affinity ranking and/or free energy predictions. Three of the datasets, Cathepsin S, JAK2 and TIE2, include a free energy prediction component.

This is an ideal opportunity to test novel algorithms on a carefully curated dataset.

Computational practices often employ a number of computational algorithms and dataset preparation steps for meaningful results. D3R will provide a forum for deposition, dissemination and discussion of such workflows through this website. Workflows will represent methods used successfully in the blinded challenges and methods donated by our pharmaceutical and/or academic collaborators. GitHub.

In Stage 1 September 1 - October 1, your predicted poses for the 24 ligands, in a coordinate system aligned with the S04-bound Cathepsin S structure provided in the inputs. Your predicted affinities, or affinity rankings, for all 136 compounds and/or your predicted absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds. When Stage 1 closes, we will release the crystallographic poses of the 24 ligands.

In Stage 2 October 1 - December 1, your predictions of the affinity rankings of all 136 compounds and/or absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds.

Full details and registration.

 

Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).

Current Version of Facio : 20.1.2 (released on August 17 2017) for Mac (Mac OS X10.6 or later and macOS Sierra)

 

The new version (2.5.0) of Gabedit has been released and is available for download at http://gabedit.sourceforge.net/

Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.

Here is a list of the significant changes between 2.5.0 and 2.4.8:

• Minor bugs fixed.

• New tools for VASP :

  • read geometries (Optimization or M. Dynamic) from VASP OUTCAR file
  • read geometry from VASP POSCAR file
  • Create VASP POSCAR file

  • Read dielectric function from a VASP xml file and compute optic properties : the refractive index n(w), the extinction coefficient k(w), the absorption coefficient alpha(w), the reflectivity R(w), the energy loss spectrum L(w), and the optical conductivity sigma(w).

    • read data from vasprun.xml and plot DOS, pDOS and, Bands structures
• Gabedit can now read the hessian from .hess orca file. After reading of the hessian, Gabedit computes frequencies, modes and effective masses.
• Export in CChemI : update
• Tv accepted (used by Gaussian and Mopac for periodic system). Using Tv, Gabedit can generate other cells.
• deMon2k is now supported (Thanks to Dennis Salahub, Mauricio Chagas da Silva, Jonathan Kung and Morteza Chehelamirani for their suggestions, corrections, comments,...)
• Gabedit can now compute the anharmonic spectrum by QM/MMFF94 method using iGVPT2 program. Gabedit can read the harmonic and anharmonic spectra from an iGVPT2 output file.
• Energy, geometry optimization, MD, MD Conformations search by MMFF94, MMFF94s, UFF and Ghemical potentials are now supported by Gabedit via Open Babel.
• Energy, geometry optimization, MD, MD Conformations search using your own program (potential) are now supported. DFTB+ is supported via this new tool.

Instructions for compiling under Mac OSX are here https://sites.google.com/site/allouchear/Home/gabedit/download/compilation-under-macosx.

 

The Schrödinger small molecule discovery suite has ben updated. This looks to be a substantial update and is described in the video below.

Supported MacOS X 10.12 and Mac OS X 10.9 - 10.11

3D Support, Supported: Interlaced stereo via Zalman 3D Monitors

 

Crystal14 Version 1.0.4 is mainly a bugfix release. All users are encouraged to upgrade to v1.0.4 as soon as possible.

This is the list of options which have been fixed in the v1.0.4 version of CRYSTAL14:

• Electronic band structure for open-shell systems (asymmetric k-points only)
• Piezoelectricity of 1D and 2D cases (non-periodic directions fixed)
• Piezoelectricity for open-shell systems
• BREAKELAST option restored
• ATOMINSE+SUPERCELL combination fixed
• Cell gradients for charged systems
• Range-separated hybrids (conflict with bipolar approximation fixed)
• Some static limits for CLUSTER option have been relaxed
• Small fixes (normalization, k-points coordinates) in phonon bands and density-of-states
• CUBE format for 3D plots of charge density and electrostatic potential fixed
• Various fixes in restart options of vibration frequencies + IR and Raman intensities calculation
• HJS exchange hole for open shell systems. This affects HSE06, HSEsol, HISS, LC-wPBE, LC-wPBEsol and LC-wBLYP functionals.
• Fixes in the POTC option

 

A recent paper describes Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability DOI

Psi4 is an ab initio electronic structure program providing methods such as Hartree–Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools.

Psi4 1.1 can be downloaded from here with versions supporting Python 2.7, 3.5 and 3.6.

Note the installation instructions for Mac: Install XCode via the App Store, Make sure you open XCode and accept the license agreement after you install.

 

The generation of multiple conformations is an important step in a number of operations from input to ab initio calculations to providing input files for docking studies. A recent paper compared seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK DOI, and also provided a dataset of ligand conformations taken from the PDB.

A recent twitter discussion involving Greg Landrum and David Koes prompted Greg to publish a blog post describing conformation generation within RDKit. The post compares using distance geometry to select diverse conformations versus an approach that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data (ETKDG). He also looks at the impact of force-field minimisation.

A really interesting read with code provided.

 

Just looking at the release notes for ADF2017 and support pages and a couple of things caught my eye.

The python distribution shipped with ADF was upgraded to python 3.5. Among others, new and updated modules include the iPython interpreter for easier development of python codes, a number of useful packages such as numpy 1.11.3 / scipy 0.18.1, ASE 3.13.0, matplotlib and RDKit 2016.09.

The Mac OSX version no longer requires XQuartz and is much faster in visualizing large systems.

 

I just got this message

We are proud to announce the 2017 release of the ADF Modeling Suite, with excellent contributions from our collaborators and the continued efforts of the SCM team in Amsterdam.

Exciting new features include
Spectroscopy-

• Many new NLO properties (TPA, THG, ...): Hu, Autschbach & Jensen
• Constrained DFT with excited states: Ramos & Pavanello
• LFDFT for d-d and d-f transitions: Ramanantoanina & Daul
• CV-DFT for singlet-triplet excitations: Krykunov, Senn, Park & Seidu
• Faster periodic response with TD(C)DFT, including 2D systems: Raupach
• VCD analysis tools: Nicu

Reactivity & Analysis-

• Latest xc functionals (SCAN, MN15-L, ....): interface to libxc 3.0
• Special points, fat bands and improved pDOS analysis
• GUI support for NEGF with BAND (Thijssen group, includes self-consistent NEGF, gate & bias potential, spin transport) and post-SCF DFTB-NEGF (Heine group)
• FDE + local COSMO: Goez & Neugebauer
• Reactivity descriptors from conceptual DFT and QTAIM: Tognetti & Joubert
• Geometry optimization with SpinFlip in QUILD: Swart
• Spin-polarization and l-dependency for DFTB: Melix, Oliveira, Rueger, Heine
• Much faster periodic DFTB(+D) optimizations, latest DFTB.org parameters freely available
• eReaxFF including explicit electrons: based on Islam, Verstraelen & van Duin
• Controllable mass-scaling for force bias Monte Carlo ReaxFF: Bal & Neyts
• Improved VLE, LLE, IDAC, kOW with reparameterized COSMO-SAC: Chen & Lin

GUI & Builders-

• Quantum ESPRESSO: GUI interface & binaries
• MOF builder and UFF4MOFsII: Coupry, Addicoat, Heine
• Much faster visualization of large and periodic systems
• Set up and visualize 'molecule gun' calculations with ReaxFF

For a more comprehensive list and details see: www.scm.com/support/release-notes

 

The latest update to ORCA has just been released.

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

New Features of Version 4.0:

New Methods:

• Linear scaling DLPNO-CCSD(T) open shell. New restricted open-shell formulation
• Linear scaling DLPNO-MP2 (RHF and UHF)
• Linear scaling DLPNO-MP2-F12 (RHF)
• Linear scaling DLPNO-CCSD(T) (the 2013 implementation is still available)
• Linear scaling DLPNO-CCSD(T) local energy decomposition scheme
• Linear scaling DLPNO-CCSD closed shell density
• Linear scaling cluster in molecule (CIM): MP2, CCSD(T), DLPNO-CCSD(T)
• Linear scaling DLPNO-NEVPT2
• NEVPT2-F12
• Updated interface to BLOCK 1.0
• DMRG-NEVPT2
• Closed shell EOM-CCSD energies
• Closed shell STEOM-CCSD energies
• Partial PNO-EOM-CCSD method for excited states
• Partial PNO-STEOM-CCSD method for excited states
• DLPNO-CCSD-F12, LPNO-CCSD-F12
• Mukherjee Mk-LPNO-MRCCSD(T)
• Powerful iterative configuration expansion (ICE-CI) approximation to Full-CI
• ICE-CI for large active space CASSCF calculations
• MREOM-CCSD (also with SOC)
• Fully internally contracted MRCI
• Full TD-DFT energies and gradient for hybrid functionals
• Super-fast approximate TD-DFT: sTDA/sTDDFT of Grimme and co-workers
• PBEh-3c method of Grimme and co-workers

SCF, DFT and Hessian:

• Large performance improvements for calculations with four center integrals
• Improved performance with RI-J with conventionally stored integrals
• Gradient for range separated hybrids
• Gradient for range double hybrid functionals with meta GGAs
• Gradient for range double hybrid functionals with range separated functionals
• Gradient for RI-JK
• Frequencies for range separated functionals
• Stability analysis and automatic search for broken symmetry states
• Local spin analysis
• Fractional occupation number analysis (FOD) for detection of MR character

MDCI module:

• All improvements for DLPNO methods as listed above
• Closed shell EOM-CCSD energies
• Closed shell STEOM-CCSD energies
• Automatic closed shell STEOM-CCSD active space selection
• EOM-CCSD(2) and STEOM-CCSD(2) approximations
• EOM-CCSD transition moments
• EOM/STEOM-CCSD core level excited states
• IP-EOM-CCSD and EA-EOM-CCSD
• ADC(2) and CC(2) methods (initial implementation)
• COSX for EOM-CCSD and STEOM-CCSD
• Improved automatic frozen core handling
• Core-correlation in automatic basis set extrapolation

AUTOCI module:

• RHF/UHF CISD
• RHF/UHF CCSD
• ROHF CISD
• ROHF CCSD
• FIC-MRCI, CEPA/0 variant and DDCI3

CASSCF, NEVPT2 and MRCI

• Detailed tutorial showing CASSCF/NEVPT2 usage
• Accelerated CI (ACCCI) a more efficient CI step for multi-root calculations
• Automatic implementation of AbInitio ligand-field theory
• Simplified generation of double-shell orbitals
• Active space protection scheme and improved warnings
• ICE-CI as CI solver for larger active spaces
• Partially Contracted NEVPT2 with and without RI
• Updated interface to BLOCK 1.0
• DMRG-NEVPT2 for active spaces up to 20 orbitals
• Magnetization and magnetic susceptibility
• Printing of the wavefunction in terms of CSFs and spin-determinants
• MREOM-CCSD (also with SOC)
• Local spin analysis for CASSCF
• Fragment decomposition of the spin-spin interaction
• Cumulant approximation for NEVPT2
• ACCCI as CIStep for FIC and DLPNO-NEVPT2
• Explicitly correlated RI-FIC-NEVPT2 (NEVPT2-F12)

TD-DFT and ROCIS:

• Full TD-DFT for hybrid functionals
• Gradient for full TD-DFT with hybrid functionals
• TD-DFT/TDA gradient with range separated functionals
• ROCIS magnetic properties (hyperfine, g-tensor, ZFS tensor, MCD)
• ROCIS-RIXS spectra
• PNO-ROCIS for spectacular performance improvements
• Super-fast approximate TD-DFT: sTDA/sTDDFT
• Natural transition orbitals in TD-DFT and ROCIS

Miscellaneous:

• GIAO implementation for NMR chemical shifts. Various aproximations (RIJOCOSX, RIJK)
• New Handling of basis set names. Now fully consistent with TurboMole def2-defaults (including ECPs) SARC basis sets separately available
• New reading of basis sets and ECPs together
• New correlation consistent basis sets added
• New SARC basis sets for the lanthanides; good for correlated calculations
• New ANO-RCC basis sets added
• Improved frozen core handling in correlation calculations
• Improved automatic auxiliary basis set generation
• Corrections for low-frequency modes in thermochemistry
• New and improved NBO interface
• CPCM and improved SMD solvent models
• Intrinsic atomic orbital (IAO) and bond orbital implementation
• Improved performance in Boys localization
• Updated and improved mapspc program
• Atomic Mean Field (AMFI) spin-orbit coupling operators
• EPRNMR works with range separated hybrid functionals
• New molecular dynamics module

 

Most drug-like molecules contain a number of rotatable bonds and prediction of bioactivities, docking etc. require an understanding of conformation. Whilst systematic methods can in theory explore all conformational space, however as the number of rotatable bonds increases a systematic search becomes prohibitive both in terms of the computational cost in generating conformations but also the time taken to process all the generated conformations (e.g. dock into protein). Thus there is great interest in rapid means to generate ensembles of representative conformations.

A recent paper DOI helps to address the problem by compiling a high quality dataset of structures generated using ligands from the Protein Data Bank.

The datasets were applied to benchmarking seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK. Substantial differences in the performance of the individual algorithms were observed, with RDKit and ETKDG generally achieving a favorable balance of accuracy, ensemble size and runtime.

The dataset is freely available for download http://www.zbh.uni-hamburg.de/?id=628

 

Chemical Computing Group have announced and update to MOE. The MOE 2016.0802 update contains a number of updates to the biomolecule modelling including improved hydrogen bond detection, and addition of a number of unnatural amino acids.

There have also been improvements to MOE/Web MOE/web. The MOE/web version compatibility check has been broadened. MOE/web license waiting has been improved. HTTPS authentication proxy server support has been improved.

 

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....

TINKER 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means TINKER can now support very large molecular systems. TINKER 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous TINKER version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of TINKER. In particular, older versions of parameter files should not be used with TINKER 8 executables and vice versa.

 

I've now written a couple of Jupyter notebooks and one of the issues that has come up is how to share the notebooks in a way that ensures the results will be reproducible in an environment when updates to components occur regularly.

Binder is a collection of tools for building and executing version-controlled computational environments that contain code, data, and interactive front ends, like Jupyter notebooks. It's 100% open source.

At a high level, Binder is designed to make the following workflow as easy as possible

• Users specify a GitHub repository
• Repository contents are used to build Docker images
• Deploy containers on-demand in the browser on a cluster running Kubernetes

Common use cases include:

• sharing scientific work
• sharing journalism
• running tutorials and demos with minimal setup
• teaching courses

If you want to find out more have a look at this blog post by the developers.

 

A nice image from the Maestro 11 training session run by Schrödinger, it looks like there are a few more training sessions coming up also.

Maestro 11 is the portal to all of Schrödinger's computational technology – far more than just a user interface, Maestro 11 also helps researchers organize and analyze data.

 

PUPIL,Program for User Package Interface and Linking, is a software environment - the program - that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be implemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

 

MolSoft have announced the release of ICM version 3.8-5.

• Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
• 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
• ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
• Support for MMTF format. The Macromolecular Transmission Format (MMTF)
• Support for Mac retina display
• Add docking restraints by selecting atoms in the receptor
• Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here

 

Chemical Computing Group have just announced an update to MOE. This release has fixed a couple of Mac OSX 10.12 (Sierra) issues but also brings a host of new features.

• MOEsaic: Web-Application for Ligand Analytics
• Spectral Analysis for Structure Determination
• Enhanced Protein Patch Analyzer
• Integrated Antibody Project Database and Antibody Homology Modeler
• Small Footprint MOE to Facilitate Large Scale Deployments
• Physical and Virtual Rendering of Structures

A more detailed description of the new and enhanced features in MOE 2016.08 can be found at http://www.chemcomp.com/print/moe2016.08.pdf.

 

The latest version of APBS includes several notable features and bug fixes. This release includes the addition of Poisson-Boltzmann Analytical-Method (PB-AM), Poisson-Boltzmann Semi-Analytical Method (PB-SAM) and the Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI). Additionally, we have made improvements to the build system and the system tests, as well as miscellaneous bug fixes.

APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules. Solve the Poisson-Boltzmann and related equations to calculate solvation energies and electrostatic properties for analysis and visualization

APBS 1.5 changes

Binary releases may be found on GitHub and on SourceForge. New Features

• Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS.
• PBSAM is currently only available in the Linux and OS X distributions.
• Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
• More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
• Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
• Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
• Included NanoShaper alternative to MSMS.
• More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
• Added binary DX format support to the appropriate APBS tools.
• Test suite amended and expanded.
• Removed hard-coded limitation to number of grid points used to determine surface accessibility.

Known Bugs / Limitations

• PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

Full details here

 

Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage.

This update contains amount other things

• Significant improvements have been made to the reasonable tautomer algorithm that affect its aliphatic and non-aromatic resonance portions.
• Inclusion of AM1BCC ELF10, a new method for applying partial charges to a molecule
• TIP3P water charges are now assigned when using Amber charge sets on molecules containing waters.

Support for Mac OS X 10.10 and 10.11 has been added.
Mac OS X 10.7 and 10.8 are no longer supported.

Full release notes are here

 

An overview of the BioExcel Project.

BioExcel is based on improving three aspects of biomolecular research. Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS (www.gromacs.org), HADDOCK (www.haddocking.org) and CPMD (www.cpmd.org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced. It’s also important to improve how easy it is for users to access and use these types of software. Not all researchers have experience in efficiently handling data and software. BioExcel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research. In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.

 

Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).

 

The GPView program is a C++ package for wave function analysis and visualization.

It is developed and maintained by Tian Shi and Ping Wang Ref](http://arxiv.org/abs/1602.07302)

In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density. The visualization module of GPView can display molecular and electronic (iso-surfaces) structures. It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files. There are also other utilities help to extract and process the output of quantum chemistry calculations. The GPView provides full graphic user interface (GUI) which makes it very easy to use.

 

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers

The Amber16 package builds on AmberTools16 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. Major new features include:

Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
Gaussian Accelerated Molecular Dynamics (CPU, GPU)
Support for external electric fields (CPU)
Expanded umbrella sampling support (GPU)
Constant pH supported with replica exchange along pH coordinate (GPU)
Support for gas phase MD (igb=6) (CPU, GPU)
Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.

 

A new version of PDB2PQR has been released.

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems

• Added alternate method to do visualization using 3dmol.
• Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/)
• Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
• Added a check before calculating pKa's for large interactions energies.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. DOI

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. DOI

 

The ADF modelling suite has been a popular modelling package used in many areas of chemistry and materials science. SCM have recently announced an important update to ADF

Software for Chemistry & Materials (SCM) is an Amsterdam-based computational chemistry software company. Originally spinning out from the Vrije Universiteit as Scientific Computing & Modelling NV in 1995, the SCM team supports and develops the ADF Modeling Suite, centered around the flagship program Amsterdam Density Functional (ADF), which was originally developed in the 1970s in the theoretical chemistry department.

Key new features::

• New XC functionals: range-separated hybrid HSE06, long-range corrected hybrids and new meta-GGAs
• SM12 solvation model and Constrained DFT in ADF
• Spectroscopy: excitations from CV(n)-DFT, fast TDDFT+TB and sTDDFT, X-ray emission, surface-enhanced ROA, new kernel for periodic TDDFT, vibrationally resolved spectra from TDDFTB, hole states in BAND
• Improved robustness for SCC-DFTB, COSMO, periodic optimizations, new HF exchange scheme
• Analysis: unrestricted and periodic energy decomposition (pEDA), Fukui functions, Natural Transition Orbitals
• Reactivity, PES: Automated reaction pathways for ReaxFF trajectories, new Transition State search options, MECP, analytic lattice gradients
• GUI: job chaining, multiple spectra, orbital interaction visualization
• Scripting: ASE interface for all codes, scripting support for COSMO-RS, job chaining, extensions to FlexMD multi-scale dynamics
• Parameters, databases: Quasinano15 including repulsive potentials for light elements, latest 3OB parameters, new parameter sets for ReaxFF, ionic liquids database COSMO-RS

Full release notes are here

 

iSpartan has been updated.

What's New in Version 1.4.6 Improved stability for iOS9 for Spartan'14 Parallel Suite (Serve)r users Enhanced charge labels in Sketch mode Increased electrostatic potential surfaces integrity

iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. The app allows any chemist fast and easy access to computational methods that have proven reliable for a large range of molecules.

 

OpenEye have announced the release of OpenEye Toolkits v2016.Feb. These libraries include the usual support for C++, Python, C# and Java.

The update address several key features.

Security

OpenEye toolkits are used in web services that require protection from malicious users. The most obvious attack vector against the OpenEye toolkits is file format parsing since scientific file formats are complex and often underdefined and there is the potential for embedded malicious code. This update closes a number of potential vulnerabilities.

FastROCS TK: Database Loading Performance

An interesting development is that physical memory limits on GPU's mean that for loading larger libraries the loading of the dataset actually takes longer than the actual search. This release addresses that issue.

OEMedChem TK

This also contains first official release of OEMedChem TK, in particular access to matched molecular pairs.

This 2016.Feb release no longer support OSX 10.8 , but support has been added for OSX 10.11. This 2016.Feb release supports Python 3.5 for the following platforms: OSX 10.10, OSX 10.11, Ubuntu 12, Ubuntu 14, RedHat 6, and RedHat 7

Full release notes are here ….

 

Added NCIPLOT to the alphabetical listing of applications. NCI (Non-Covalent Interactions) is a visualization index based on the density and its derivatives. It enables identification of non-covalent interactions. NCIPLOT is available for download.

Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.

 

WebMO version 16

WebMO version 16 has been officially released and is available for FREE download at http://www.webmo.net/download

New features in WebMO version 16 include:

• Support for both iOS and Android WebMO free apps
• Support for the newest versions of ORCA, PSI, and Q-Chem
• Support for hydrogen bonds in the WebMO editor
• Improved support for building/cleanup of fused aromatic rings
• Incorporation of modern HTML5 user interface elements including: drag-and-drop of jobs between folders, fewer pop-up windows, live updating of output files while jobs run, and expandable results page
• Support for unlimited number of user folders and sub-folders (Pro)
• Enhanced support for resource specification with external batch queues (Enterprise)
• Various bug fixes

Important changes in the previous version include:

• Java security warnings are reduced/eliminated with new signed applet
• Support for the newest versions of GAMESS, MOPAC
• Lookup feature to build structures by name (type "aspirin" or "vancomycin")
• Links to external databases to lookup molecular properties, spectra, and data
• Huckel molecular orbital calculations from within Build Molecule page (Pro)

WebMO is the most popular interface to computational chemistry programs, with over 22,000 unique WebMO licenses issued to date!

WEBMO iOS AND ANDROID APPS

WebMO has released a new Android app and updated its popular Apple iOS app!

The WebMO apps for portable devices are FREE.  

The Android and iOS WebMO apps provide equivalent features including:

• Standalone molecular editing, optimization, symmetry, and orbital calculations
• Integrated web lookup of molecular properties, spectra, and data
• Access to WebMO servers (Free, Pro, and Enterprise versions of WebMO 16 and higher)

The WebMO apps supports all chemistry courses by calculating and displaying:

• VSEPR structures for General Chemistry
• 3-D structures to replace model kits for Organic Chemistry
• Data and properties for Analytical Chemistry
• Point group and symmetry elements for Inorganic Chemistry
• Small proteins and bimolecules for Biochemistry
• Molecular orbitals and vibrations for Physical Chemistry
• WebMO calculations for undergraduate and graduate level Research

Thousands of students and scientists use the WebMO apps on their smartphones and tablets each month.  You can join them today for free!

WEBMO SUPPORTS CLOUD COMPUTING

More computational services are moving away from local hardware and into the "cloud".  Cloud computing requires zero upfront capital outlay, eliminates hardware maintenance, and can dramatically lower the cost of computing.

WebMO now supports installation on cloud computing platforms.  In less than 10 minutes, you can use your web browser to create a virtual machine, run the WebMO SITC ("Server in the Cloud") script, and have a functioning WebMO 16 server.

The cost of a WebMO cloud server can be amazingly low: <$1 per day for a WebMO server capable of running jobs on standard ab initio chemistry engines, and just $0.12 per day for a WebMO server running MOPAC!  And when you don't need it, you just turn it off.

Complete documentation is available at http://www.webmo.net/cloud/sitc.html

Since Google Compute Engines are free for the first 60 days, so there is no cost or risk to try cloud computing today.

 

Sampling conformational space is a key requirement for several areas of ligand design in small molecule drug discovery. A recent paper BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library DOI describes a new conformational search method.

The project homepage provides a download, supports Mac OSX 10.4 or higher.

 

The current version is CCP4 7.0 (07 January 2016). The new packages include:
SHELX suite: co distribution for academic users
CCP4I2: new ccp4 interface
DIALS: data processing and integration
ARCIMBOLDO-LITE: molecular replacement pipeline
The updated packages include PHASER, XIA2, REFMAC, MONOMER LIBRARY, AMPLE, COOT, AIMLESS POINTLESS, CTRUNCATE, DIMPLE, BLEND and many more

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

The latest version supports Mac OSX and Linux and requires X11. Source code is also available.

 

Chemical Computing Group have just released an up date to MOE, version 2015.10 includes:-

Protein-Protein Docking

• Generate docked poses using FFT followed by all atom minimization
• Define receptor and ligand sites to focus docking
• Automatically detect antibody CDR sites

Integrated Alignment, Consensus and Superposition in the Sequence Editor

• Manipulate multimeric protein sequences using split side-by-side Sequence Editor panes
• Use dendrograms to visualize pairwise similarity, identity and RMSD relationships
• Select residues based on plotted values using resizable sequence editor plots

Distributed Pharmacophore Searching

• Run pharmacophore searches on a cluster directly from MOE GUI
• Perform fast corporate database searches
• Access multiple databases stored on a central server

Covalent Docking and Electron Density Docking

• Use reaction-based organic transformations to covalently docking
• Minimize ligand strain energy while maximizing ligand fit to electron density
• Run docking through an enhanced streamlined scenario-based interface

Extended Hückel Descriptors and pKa Model

• Compute molecular properties such as logP, logS and molar refractivity
• Determine populations of ligand protonation states at a given pH
• Calculate the pKa and pKb of small molecules

13C NMR Analysis

• Apply QM conformation refinement to calculate 13C NMR shielding
• Convert computed shieldings and predict 13C NMR chemical shifts
• Compare computed chemical shifts to experimental shifts for structure determination

I'll write a review in the New Year.

 

I just thought I'd flag a recent paper on sampling conformation space DOI.

The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships.

The software is available from the MeilerLab home page

 

OpenEye have announced the release of OpenEye Toolkits v2015.October. These libraries include the usual support for C++, Python, C# and Java.

New Features

• FastROCS TK was added to the OpenEye toolkits collection
• Molecule reading performance improvement in OEChem TK
• The capabilities of the OEBio-Fragment Network have been expanded
• 213 new ring templates have been added to the OEChem TK built-in ring dictionary

The full release notes give more details

In particular note the 2015.Oct release is the last to support Mac OSX 10.8 so time to upgrade if you have not already done so.

 

The Medicines for Malaria Venture have an interesting page in which they are accumulating a list of computational tools and guides describing the use of the tools to address key issues within the drug discovery process.

Tools were chosen to address common needs expressed by medicinal and computational chemists working in the not-for-profit area. Recognising that this is a global effort, we have selected software packages on the basis of being free for all users.

The guides are either text descriptions or webcasts showing the tool in action. To date they include DataWarrior, KNIME, YASARA, ChEMBL and PK Tool.

 

The Dalton2015 suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilities.

Together, the two programs provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2015 suite.

Dalton can be run on a variety of systems running the UNIX operating system. The current release of the program supports Linux, Cray, SGI, and MacOS using GNU or Intel compilers (we plan to publish patches for PGI and XL compilers).. The program is written in FORTRAN 77, FORTRAN 90 and C, with machine dependencies isolated using C preprocessor directives. All floating-point computations are performed in 64-bit precision, but if 32-bit integers are available the code will take advantage of this to reduce storage requirements in some sections.

 

The popular GUI for GAMESS MacMolPlt has now been renamed and moved to GitHub, wxMacMolPlt is a cross-platform (Mac OS X, Linux and Windows) GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties

wxMacMolPlt can be downloaded from here

Bode, B. M. and Gordon, M. S. J. Mol. Graphics Mod., 16, 1998, 133-138. DOI

 

SeeSAR 3.2 can now be used in cases where there is no protein. For example if for the analysis of a ligand-based virtual screen

Release Notes version 3.2 2015-07-24

Utilizing SeeSAR without a protein

• SeeSAR has grown from a single purpose affinity assessment tool to a multi purpose 3D structural viewer for compound design and prioritization. With this update it is now also possible to use all these nice features for 3D ligand-based projects. You may, for example, visually inspect small molecules alignments. You may filter a hit list by means of calculated and external properties...
• Big data booster, With version 3.0 we first equipped SeeSAR with database functionality. Version 3.2 comes with a load of performance enhancements that speed up the calculation by up to a factor of 5, now utilizing all available CPUs in your computer even more efficiently.
• 3D graphics enhancement, In this version we updated the graphics support and SeeSAR is now compatible with more graphics cards than ever before. Especially the compatibility with integrated graphics cards (the type most frequently found in laptop computers) - which used to be the major trouble makers - has been greatly improved.

 

Kinetiscope is a scientific software tool that provides the bench scientist with an easy-to-use, rapid, interactive method for the accurate simulation of chemical reactions.

The program package is completely self-contained, and requires no programming or extensive user training. This lets you become immediately productive,

Kinetiscope comes with a User's Manual, a set of tutorials and an extensive library of example simulations that show you the kinds of systems that can be studied with it and that illustrate techniques for handling various types of physical situations. The library includes simulations of gas phase, solution phase and solid state reactions such as co- and terpolymerization ... radical chain-initiated polymerization (including a sample spreadsheet for extracting molecular weight distributions) ... kinetic resolution of enantiomeric mixtures ... chemistry in supercritical media ... pH-dependent model enzyme kinetics ... thermogravimetric analysis ... temperature programmed desorption ... smog chemistry ... silane chemistry in a chemical vapor deposition reactor ... model batch and flow catalytic reactors ... curing of polymers with significant volume shrinkage ... synthetic protocols for preparation of a photosensitizer ... chemical oscillators ... electrochemical reactions studied by cyclic voltammetry ... photochemical reactions from a pulse light source ... pharmacokinetics of drug dosing ... and imaging chemistry in photoresist materials.

Kinetiscope is a 64-bit application and requires Mac OS X 10.6 or above.

• D. L. Bunker, B. Garrett, T. Kliendienst and G.S. Long III, Combustion and Flame 23, 373 (1974).
• D. T. Gillespie, Journal of Computational Physics 22, 403 (1976).

 

I just thought I'd mention this upcoming workshop, as ever there is a top class line up.

EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery 2-6 November 2015 Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=510

The draft agenda is here

 

SeeSAR has been updated to version 3.1, the release notes highlight two significant new features.

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution.

• Working with "big data" With this update we lifted the limit of handling only a maximum of 5000 poses in SeeSAR. We know that a lot of people like to do their compound analysis and prioritization after virtual screening campaigns also with much bigger sets. It is not likely that you will look at more than a couple of hundred poses, however, since the filtering (see also below) is extremely efficient, it provides quite an attractive opportunity to load all your data (not just the top x) and do your prioritization with all properties at hand right here in SeeSAR.
• Enhanced filtering Behind the scenes SeeSAR knows so much more about your compounds than what is displayed in the table. The basic stuff like no. of acceptors and donors, rotatable bonds, etc. to do the usual Lipinski-type filtering is of course available, but also more elaborate stuff like the number of hydrogen bonds formed or the number of torsions that lie outside the statistical "norm". All of these are now available for filtering to help you optimally trim down your data to find the really interesting part.

NOTE! SeeSAR project files from older versions are incompatible and cannot be loaded. By default SeeSAR puts a new version in a separate location. The recommendation is to export your data from the old project file with the old version and import it into the latest SeeSAR. This is a one-time effort, which allows you to benefit from the features of the most up-to-date version.

 

Findings 1.2.3 the electronic notebook has just been released. Already using Findings? Menu Findings → Check for updates...

OpenEye have just announced the release of SZMAP v1.2.1. This is a critical upgrade that fixes several bugs.

• The Water Orientation VIDA Extension now saves orientation probability data and ensemble energy, vdw and order data on probe molecules as SDData. When probes generated by this extension are written to an .sdf file, these values will be written as well.
• The Water Orientation VIDA Extension (version 1.1.3) now displays the correct water orientations for results from szmap version 1.2.0. It is also more compatible with 2D depictions in the 3D display.
• gameplan no longer crashes when all stabilization test sites clash.
• pch option -nonsymmetrized_charges now works to control AM1BCC partial charges. The default has been changed to true so as not to alter the default behavior.
• pch no longer treats CYS residues bonded through the sidechain to a non-CYS as anionic.
• pch no longer duplicates non-standard groups containing a metal (such as cofactors) and groups they are bonded to.
• The hydrogen charge on the standard water probe is now correctly listed as +0.327 not +0.237 in SZMAP Theory.

 

The update of Forge, a computational chemistry workbench for ligand-based design, includes over 170 new or improved features. Of particular note is Activity Atlas a new component enables you to summarize the SAR for a series into a visual 3D model that can be used to aid new molecule design. Forge V10.4 can now connect to an external web service, through a REST interface, to import external properties and data computed or retrieved by such web services as additional columns in the Molecules Table.

The latest version of Torch now includes Multi-parameter Optimization (MPO) options including condensing many activity and physicochemical properties into a single score representing the fit to the project profile, this has been coupled to an improved radial plot visualisation and tile display.

 

OpenEye has announced the release of OpenEye Toolkits v2015.June. These libraries include the usual support for C++, Python, C# and Java and are now available for download.

New Features Highlights:

• PDB Splitting in OEBio TK
• PAINS (Pan Assay Interference Compounds) filter in OEMolProp TK
• Matched molecular pair improvements in OEMedChem TK
• Custom ring template dictionaries in OEChem TK
• Anaconda support for easier Python toolkit installation

 

The recently updated AMBER tools now includes software to analyse the structure and thermodynamics of water at protein and other surfaces. In addition to 3D-RISM, AMBER Tools now includes a new method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites.

The method is described in this paper, Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril DOI.

Solvation and desolvation plays a critical role in ligand binding but can be difficult to determine computationally.

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.

 

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. In an interesting development it is now possible to compile Gamess-US on the $40 Raspberry Pi, full instructions are available here. This provides a low cost system for demonstrating quantum chemistry.

To aid construction of the chemistry input WebMO-14.0, a web-based interface for computational chemistry programs, now has an App for iPhone/iPad. This allows you to compose e.g. a Gamess computation on your iPad or iPhone and send it to your Raspberry Pi (in the local network or on the web with a forwarded IP) to run the job and get the results back for visualizing and printing.

 

I just got this message regarding MacMolPlt a graphics program for plotting 3-D molecular structures and normal modes (vibrations).

I have just finished posting the final binaries for MacMolPlt 7.6. In addition to the code changes I have had to move the home site and binaries download sites due to the impending shutdown of Google code.

This version includes the following changes:

• Energy plot window now accepts the same keystrokes as the main display window to change frames (left, right, home, end)
• Fix a parsing issue with ROHF GAMESS log files
• Account for an $EFRAG group change to allow all fragment atoms rather than only the first three.
• Fixed a crash in the frequency window (when no normal modes are present)
• Fixed the positioning of lone pairs in the builder when the coordination number plus the number of lone pairs is 5.
• Fixed a couple of parsing issues with MolDen and Molekel (mkl) files.
• Added GIF and TIFF export image formats (requires wxWidgets 2.9 or newer).

I have also reworked the 3D orbital generation code to significantly improve performance. Please report anything that doesn't look quite right.

Binaries and source files are available at: http://brettbode.github.io/wxmacmolplt/

 

Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.

Journal of Cheminformatics 2015, 7:16 [DOI](http://dx.doi.org/10.1186/s13321-015-0060-z}

The source code is available on Sourceforge

 

I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.

 

MOE2014.0901 Update is now available. MOE is a fully integrated molecular modelling and drug discovery software package.

MOE 2014.0901 updates:

Enhancements:

Protein Builder

• Option for AMBER residue name
• Append/prepend multiple residue sequence specified by single-letter names Builder:
• Added H’s inherit color if there is a consistent coloring in the residue

sddesc: New -smi:p option causes field headers to be written to the output ASCII file

Bug Fixes:

• MOESVLRUNPATH now properly honored
• Combinatorial Builder now honors different attachment point locations on the same R-group
• Database Save As one entry per file mode now properly generates unique filenames
• Dock Template Forcing batch file now correctly generated
• Saved views in .moe files now properly restored
• Auto-save when Database Viewer display attributes are changed can now be disabled to prevent changes to the database file modification date when only the display is changed and not the database content
• SVL function Deprotonate now works properly
• Various MOE Project and Project Database Update bugs
• Various minor bug fixes

There are reviews of MOE available here

Moe:- Molecular modeling
Moe Update (Jan 2009):- Molecular modeling
Review of MOE (2009.10 release):- Molecular modeling
Moe Update (December 2010.10 release):- Molecular modeling
Moe Update (December 2011 release):- Molecular modeling
Moe Update (December 2012 release):- Molecular modeling

 

The molecular modelling platform MOE 2014.09 has been updated, some of the new features in MOE include:

• MOE Project for Organizing SBDD Data
• Focused Protein and Antibody Libraries - Virtual Phage Display
• Quantum Mechanical Refinement of Conformations and Energy Minimization
• Template Forced Docking and Molecular Superposition
• Non-natural Amino Acid Support for Protein and Peptide Design
• Specialized Protein Family Databases and Search Interface

MOE is a software system designed to support Cheminformatics, Molecular Modelling, Bioinformatics, Virtual Screening, Structure-based-design and can be used to build new applications based on SVL (Scientific Vector Language).

There are several reviews of the previous versions of MOE here

 

Previously known as StarVue, the latest release of Ocura, version 6.0, is now available. This latest release will enable you to open and view files from the latest releases of StarDrop 6.0 and Sentira 1.0.

Ocura is a desktop application is specifically designed for scientists who want a simple way to load a set of molecule structures and easily browse through the data.

 

OpenEye ihave announce the release of POSIT v3.1, the component of the OEDocking suite devoted to pose prediction.

This update includes:

• The HYBRID and FRED algorithms have been incorporated into POSIT, the appropriate method is determined by analyzing the ligand to pose against the input receptors.
• Multiprocessing has been enabled through the use of MPI, to speed calculations.
• POSIT now supports a list of receptors files or .lst file as input. This overcomes command-line limitations for the number of receptors that can be used simultaneously.
• Added a MEDIOCRE result rating for results between 33% and 50% probability.
• Command line parameters have been simplified and updated to be compatible with the OEDocking Suite of tools.

POSIT is designed for the posing problem in lead optimization, i.e. how best to leverage project information from previous protein-ligand structures to predict the pose of a new ligand. It does this by assessing the similarity of the new ligand to known bound structures. Performance degrades as similarity decreases and so at some point it is worth searching more exhaustively.

 

SeeSAR 1.5 has been released. SeeSAR it is intended as an interactive tool for designing/improving ligands for drug discovery.

The latest release covers two major topics: 1. A series of features that make the editing more swift and easier. To this end they introduced hot-keys, context menus and drawing a bond by drag&drop. 2. Often times people use SeeSAR for visual inspection e.g. after docking. Now normally you'll have multiple poses per compound. For a better overview the Table now allows you to collapse all poses to just one line per compound.

Furthermore you can set a bookmark to indicate what you like and export only the ones on the wish list.

There is a review of SeeSAR here.

 

I just got this email

Thank you for your collaboration in helping us to test the beta version of the FORECASTER Suite 2014. From your feedback and bug reports, we have now released the final version of the Suite. The files were updated and posted on the download page. Please send us any bugs that you might have not yet reported.

The FITTED docking tool was initially been developed as a suite of three programs: SMART (used to prepare the small molecules for docking), PROCESS (used to prepare the protein files for docking) and the docking program FITTED. More recently, these three programs together with several others have been integrated into a single package, namely FORECASTER.

More information can be found here http://fitted.ca/download.html#forecaster

 

The ADF modeling suite consists of the GUI, the powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), the semi-empirical DFTB and MOPAC2012 modules, ReaxFF, and COSMO-RS. The binaries for the entire suite work out of the box, in parallel, on all popular platforms (Windows, Mac, Linux).

A summary of new features and improvements in the 2014 release:

• lower-memory, better parallel SCF in ADF
• significant speed-ups in DFTB and the periodic DFT code BAND (AO-based)
• many-body dispersion functionals (Tkatchenko et al.)
• conformer search, support for multiple configurations, spectra averaging
• TD-DFTB and DFTB-NEGF, with electronic parameters for 87 elements
• ReaxFF force field optimizer, Grand Canonical Monte Carlo
• COSMO-SAC 2013-ADF parameters

 

KiSThelP is a cross-platform free open-source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, NWChem). Some key features are:

• gas-phase molecular thermodynamic properties (offering hindered rotor treatment)
• thermal equilibrium constants
• transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart)
• RRKM rate constants, for elementary reactions with well-defined barriers.

KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the GUI and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D-plots, exporting images and data files.

 

Sentira is a new chemical data visualisation tool from Optibrium. The focus is on ease of use data visualisation and as such is probably targeted at the bench scientist rather than a specialist computational scientist. It supports a selection of plotting and SAR tools.

I’ve written a review of my first impressions.

There is also a list of data visualisation applications here.

 

Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions

The DDEC method is described in the following publication and references therein.

Thomas A. Manz and David S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials", J. Chem. Theory Comput., Vol. 8 (2012) 2844-2867. DOI

The program can be run using either Matlab or Fortran source codes, which yield identical numbers. The Fortran code is parallelized with OpenMP and runs much faster than the Matlab code.

 

Quantum Expresso 5.1 is available for download.

QUANTUM ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modelling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

 

McQSAR:  A Multiconformational Quantitative Structure−Activity Relationship Engine Driven by Genetic Algorithms

McQSAR, an extension to the traditional GA approach to derive QSARs. McQSAR is able to use descriptors for multiple representations per compound, such as different conformers, tautomers, or protonation forms. Test runs show that the algorithm converges to a set of representations that describe the binding mode of the set of input molecules to a reasonable resolution provided that suitable descriptors based on the three-dimensional structure are used.

Mikko J. Vainio and Mark S. Johnson (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J. Chem. Inf. Model. 45, 1953-1961 DOI.

The recently updated Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.

 

One of the advantages of using a Mac for science is that you can often make use of the UNIX underpinnings of Mac OSX to access programs written for Linux.

A recent publication in Journal of Cheminformatics caught my eye, screening of molecules using electrostatics is usually a very time-consuming process, but this publication describes an interesting and very quick way to screen molecules.

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening Francois Berenger, Arnout Voet, Xiao Yin Lee and Kam YJ Zhang Journal of Cheminformatics 2014, 6:23 doi

I’ve written instructions for how to install ACPC under Mac OSX.

 

Now that I have my new MacPro I thought it might be interesting to try out a couple of the software packages that I’ve previously reviewed. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds. I’ve previously reviewed ForgeV10 and as it was formally known FieldAlign so I’m going to focus on the support for multiple processors and a few of the new features.

Read the review here

There is a compilation of software reviews here

 

Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

• Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
• Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
• A completely reorganized Reference Manual
• QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
• More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
• Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
• New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

• The sander module, our workhorse simulation program, is now a part of AmberTools;
• Greatly expanded and improved cpptraj program for analyzing trajectories;
• new documentation and tools for inspecting and modifying Amber parameter files;
• Improved workflow for setting up and analyzing simulations;
• new capability for semi-empirical Born-Oppenheimer molecular dynamics;
• EMIL: a new absolute free energy method using TI;
• New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
• Completely reorganized Reference Manual

 

A recently publication “High Performance in silico Virtual Drug Screening on Many-Core Processors” DOI describes porting BUDE (Bristol University Docking Engine) to OpenCL.

Our highly optimized OpenCL implementation of BUDE sustains 1.43 TFLOP/s on a single NVIDIA GTX 680 GPU, or 46% of peak performance. BUDE also exploits OpenCL to deliver effective performance portability across a broad spectrum of different computer architectures from different vendors, includ- ing GPUs from NVIDIA and AMD, Intel’s Xeon Phi and multi-core CPUs with SIMD instruction sets.

BUDE is now one the fastest HPC applications ever developed and nicely demonstrates the portability of OpenCL across different architectures.

There is a list of GPU accelerated applications here.

 

CrunchYard is pleased to announce their academic offering for HPC in the cloud. The academic offering allows anyone with a valid academic e-mail to instantly access the online HPC facility.

Group accounts can be created for your research group, where simulation credits are shared. Credits are valid for 2 months after purchase.

Academic accounts include access to over 300 true CPU cores, and the following simulation software: FEKO CP2K NWCHEM GAMESS GROMACS LAMMPS

Other licensed codes are available on request (such as CPMD, STAR-CCM+ etc.)

 

The official mobile app for viewing PDB structures RCSB PDB has been updated to include the April molecule of the month.

The molecule designer app Asteris has been updated to version 1.0.1 with a number of bug fixes and performance improvements.

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

• Pure QC simulations - ab initio and SMO.
• Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
• Hybrid QCMM simulations.
• Single point calculations.
• Energy minimization.
• Molecular dynamics.
• Reaction coordinate scanning.
• Umbrella sampling.
• Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

• pDynamo
• Matplotlib
• Numpy / Pylab
• Pymol 1.x
• pyGTK
• ORCA, ab initio calculations.

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

 

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03/09, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported. The following analyses are available:

• The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, Molpro, and ORCA,
• Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
• Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital,
• Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
• Frenking’s Charge Decomposition Analysis,
• Calculation of Mayer's bond orders,
• Visualization of each step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
• Plots of Convergence and Energy in the Geometry Optimization tab,
• A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
• Animation of the normal modes of a frequency calculation and the ability to save these as animated GIFs,
• Plots of IR and/or Raman spectra in the Frequency Tab, and
• A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.

QMForge has been created using the following dependencies:

• The Python scripting language (2.7.5),
• The Qt4 toolkit and its Python extensions PyQt4,
• NumPy (1.7.1),
• PyQwt (5.2.0), and
• The cclib computational library (v1.2b).
• OpenBabel and its Python bindings
• The Python Imaging Library (PIL)
• simplejson

QMForge has only been extensively tested on Mac OS X Snow Leopard and Mavericks

Tenderholt, Adam L. QMForge, Version 2.3.2, http://qmforge.sourceforge.net.
Tenderholt, Adam L. "QMForge: A Program to Analyze Quantum Chemistry Calculations", Version 2.3.2, http://qmforge.sourceforge.net.

 

The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
phasefqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical.py script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see http://tech.knime.org/whats-new-in-knime-29 for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.

 

MolSoft have announced that a new version of ICM is now available for download from the support site . A description of the key new features can be found on the news page and release notes. To help you get to know the new features we will be holding a free webinar next week (2/11) - we hope you can join us, please register here.

Some of the key new features include:

• Anaglyph Stereo
• MolSkin - high quality surface graphics
• Movies from Slides
• SCARE - induced fit docking
• Fragment screening
• MolScreen - >360 high quality fingerprint and 3D pharmacophore models
• Blast search direct from the GUI
• ToxScore - new score for drug reactivity and toxicity

 

QMForge 2.3.1, a cross-platform, open-source program for interpreting and analyzing the results of QM calculations has just been released

QMForge 2.3.1 builds upon the previous versions with the addition of the following features:

• Plots of Convergence and Energy in the Geometry Optimization tab,
• Plots of IR and/or Raman spectra in the Frequency Tab,
• Ability to save the normal modes of a Frequency calculation as animated GIFs,
• Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital

Other notable features include

• The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, and ORCA,
• Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
• Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
• Charge Decomposition Analysis,
• Mayer's bond orders,
• Visualization of every step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
• A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
• Animation of the normal modes of a frequency calculation, and
• A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.

 

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues to resolve in drug discovery often revolve around absorption, distribution, metabolism and excretion (ADME). Whilst we can measure the levels of parent drug in various medium tracking metabolic fate can often be a considerably more difficult proposition requiring significant resources. For this reason prediction of sites of metabolism has become the subject of current interest.

FAME DOI is a collection of random forest models trained on a comprehensive and highly diverse data set of 20,000 small molecules annotated with their experimentally determined sites of metabolism taken from multiple species (rat, dog and human). In addition dedicated models are available to predict sites of metabolism of phase I and II processes.

FAME offers a high performance prediction of sites of metabolism mediated by a wide variety of mechanisms.

The full review is available here

There is a list of software reviews here.

 

Chemical Computing Group have just announced an update for MOE.

A patch update is now available for MOE 2013.08. This patch contains a series of important updates for better performance, s

In the MOE 2013.0801 patch update:

• System Manager browsing speed-up for large systems
• System Manager tag/group expansion only on Ctrl-click during browsing
• Mac OS X NVIDIA graphics driver bug workaround
• Mac OS X real-time ray tracing now supported by default on the new Intel Iris and Intel Iris Pro graphics cards
• Bug fixes

 

I recently came across this brilliant collection of software from Michel Petitjean

• ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
• ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
• CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
• CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
• CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
• DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
• DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
• GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
• MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
• POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
• POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
• QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
• RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
• VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.

Binaries are available for MacOSX and Linux.

 

I noticed that CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on Crunchyard expanding the list of available Computational Chemistry packages. The following packages are also available. CP2K, LAMMPS, GAMESS, GROMACS , NWCHEM

I’ve added CPMD to the alphabetical listing of applications.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.

Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

CPMD capabilities

• Works with norm conserving or ultrasoft pseudopotentials
• LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
• Isolated systems and system with periodic boundary conditions; k-points
• Molecular and crystal symmetry
• Wavefunction optimization: direct minimization and diagonalization
• Geometry optimization: local optimization and simulated annealing
• Molecular dynamics: constant energy, constant temperature and constant pressure
• Path integral MD
• Response functions
• Excited states
• Many electronic properties
• Time-dependent DFT (excitations, molecular dynamics in excited states)
• Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.

 

SYBYL-X 2.1.1 is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.

1. Hologram QSAR (HQSAR) is a now available via Python.  HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors.

2. Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.

 

OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

• New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
• A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
• Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
• Constraining torsion potential in the form: , where is the user specified force constant and is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
• New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
• Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
• New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
• Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
• Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.

 

Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).

General Updates

Extended Hückel Theory for Pharmacophore Discovery

• Apply EHT strengths to identify and discover weak and strong interactions
• Annotate non-standard interactions: halogen and CH bond donors
• Score pharmacophore hits using sum of interaction energies

de novo Loop and Linker Modeler

• Search and browse for de novo and knowledge-based loop candidates
• Generate multiple loop conformations and score loop-loop interactions • Investigate linkers for fusion proteins and dual variable domains

Protein Alignments and Superpositions

• Superpose protein structures independent of sequence
• Apply new threading methodology for sequence to structure alignments
• Align sequences and superpose structures using STOVCA criteria

Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.

• Create additional data grouping level in System Manager
• Handle large number of protein:ligand complexes in real-time
• Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored

Interface to Mogul from CCDC

• Access a knowledge-based library of small molecule crystallographic data
• Visualize histograms and statistics fo rbond angles, dihedrals and torsions • Ensure ligand conformation is consistent with the CSD

Solvent Analysis using 3D-RISM Enhancements

• Calculate water densities on full protein or protein:protein interface
• Accurate placement and stability prediction of water sites
• Use3 D-RISM densities to validate water position in crystal structures

chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies

Mac OS X Enhancements.

1. OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations – Hide, Show, and Quit – across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.

2. New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.

3. Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.

 

OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.

There are also a number of already built models that the public can access, these include

• Ames test
• CYP1A2 inhibition
• LogP and Solubility

You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.

 

Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-

“What is the largest change that can be made whilst maintaining activity?”

Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge. Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

More details are here

 

OpenEye have just announced that the virtual screening tool ROCS v3.2 has been released.

Several noteworthy features have been added to this version including a -subrocs option that can drastically improve substructure alignments. Also included is an application rocs-report that uses our 2D depiction technology to make pdf reports of hitlists displayed with 2D similarity, shape and color overlaps, as well as property histograms. Substantial upgrades have been made to vROCS. An improved sketcher now highlights unspecified stereochemistry in atoms and bonds in query structures, and requires the user to correct any unspecified stereochemistry.

ROCS is available for download here.

StarDrop was recently updated to version 5.4, this brings an update to the virtual library design module and scaffold based design, there have also been improvements to the plotting and data visualisation.

There are now seven optional plugins with three exciting new options.

Derek Nexus™ - Knowledge based toxicity prediction The new Derek Nexus module for StarDrop provides Lhasa Limited's world-leading technology for knowledge-based prediction of key toxicities. Using data from published and donated (unpublished) sources, Derek Nexus identifies structure-toxicity relationships that alert you to the potential for your compounds to cause toxicity. The Derek Nexus module provides predictions of the likelihood of a compound causing toxicity in over 40 endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.

BIOSTER™ - A world of chemistry experience BIOSTER is developed and updated in collaboration with Digital Chemistry and is available as an optional extension to StarDrop's Nova module. This combination enables you to quickly and easily search the comprehensive BIOSTER database to identify transformations that are relevant to your compounds. These can be automatically applied to generate novel structures with a high likelihood of biological activity and synthetic accessibility, prioritised against the property profile you require for your project. BIOSTER brings the collective experience of the chemistry community to help you to discover new active analogues of your compounds based on the tried and tested principle of isosterism. The BIOSTER module contains a unique compilation of over 20,000 precedented bioisosteric transformations, manually curated from the literature by Dr István Ujváry, complete with references to the original publications in which they are described.

torch3D™ The renamed torch3D module, using Cresset’s unique Field technology to understand and apply 3D Structure Activity Relationship (SAR), has been updated to include the latest version of Cresset’s XED force field providing insight into compounds’ 3D structures, biological activities and interactions.

These certainly significantly expand the potential utility of StarDrop, but note that these are not part of the standard install and may require additional licensing.