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?
Modeller written in Fortran90 has been ported to Apple Silicon
They used the gfortran that's part of the gcc homebrew package (https://brew.sh/). They see about a 20% performance improvement with gfortran-10 on a 2020 Mac Mini (M1) compared to Intel Fortran on a 2018 Mac Mini (Intel).
MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.
If you are using the Homebrew package manager, you can install Modeller on recent Macs (either Intel or Apple Silicon, M1) by simply running
brew tap salilab/salilab brew install modeller
NEW & ENHANCED FEATURES IN MOE 2020.09
- High Throughput Docking to Screen Large Data Sets
- Protein Liabilities Predictions using Ensemble Averages
- HPC Framework to Launch Large Calculations
- MOEsaic: Free-Wilson Analysis to Generate Virtual Compounds
- QM/MM Calculations with ONIOM
- Enhanced Antibody Annotation and Classification
More details are here https://www.chemcomp.com/Products.htm
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.
Someone just pointed out to me that you can now install AmberTools20 using conda.
conda install -c conda-forge ambertools=20
This should work for Linux and MacOS systems, but it does not provide access to parallel or gpu-optimized codes. It provides a simple way to get started with AmberTools, and to install it into many workflows, but is not a substitute for the full source-code distributions
Full details are here http://ambermd.org/GetAmber.php.
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)
- 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
- 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
About a year ago I wrote a review of Flare a tool for structure-based drug design.
The key new features of Flare V4 includes significant improvements to Free Energy Perturbation (FEP), new and improved force fields, new Dynamics analysis tools, plus new and improved GUI functionality.
The implementation of the Open Forcefield now allows users to update themselves.
FEP has been implemented in Flare DOI and this release improves performance.
In terms of speed, all FEP calculation in Flare V4 are significantly faster thanks to an improved algorithm with a 20% increase in performance, and they are fully parallelizable. This means that each bit of the transformation of one compound into another (the lambda windows) can be run on separate GPUs: the results will be merged at the end of the calculation. This can bring the calculation time for a single transformation on a medium-sized protein to less than 2 hours on a small cluster of 10 GPUs (for example AWS g4dn.xlarge, Tesla T4 spot instances).
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?.
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 email@example.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 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.
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.
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.
I came across this website recently https://www.ks.uiuc.edu/Research/cloud/, describing efforts to harness cloud computational resources.
The use of advanced molecular simulation techniques often comes with additional computational and software requirements. Running molecular simulation and analysis tasks in the Cloud can significantly lower the barriers to use of advanced simulation methods and provides a cost-effective and practical solution for many molecular modeling tasks and for small and moderate size molecular dynamics simulations.
There are detailed instructions for accessing Amazon web services EC2, both GPU and CPU hardware.
We have adapted our molecular modeling applications NAMD, VMD, and associated tools to operate within the Amazon Web Servers (AWS) Elastic Compute Cloud (EC2) platform, enabling popular research workflows such as MDFF structure refinment and QwikMD simulation protocols to be run remotely by scientists all over the globe, with no need for investment in local computing resources and a reduced requirement for expertise in high performance computing technologies.
Well worth a browse.
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.
Chemical Computing Group have announced the 2019 release of PSILO, CCG Protein Structure Database System. The PSILO 2019.02 version includes a variety of new features and enhancements for viewing and searching records and for aligning and identifying protein active sites. Additional features in PSILO 2019.02 include streamlined PSILO IT infrastructure which facilitates deployment and performing PSILO searches directly from MOE.
NEW & ENHANCED FEATURES IN PSILO 2019.02
- Analyze Ligand and Receptor Interaction Patterns using Clustered 3D Environments
- Perform the Full Range of PSILO Searches from MOE
- Infer Apo-pockets Using PSILO Family References
- Include Crystal Contacts in Ligand Interaction Diagrams
- Streamlined PSILO IT Infrastructure
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.
SeeSAR a structure-based design tool has been updated.
Version 9 represents another major leap in SeeSAR's evolution, fully adopting the 'modes' concept. Molecules can be transferred freely between modes as you carry out various different tasks. This gives you much more flexibility while maintaining a structured overview. To help you keep track of where you are, we distinguish the modes using a beautiful backlit color scheme, focused top center on the mode switch but found throughout the tool to guide navigation.
The latest update to the popular chemical 3D modelling and visualisation tool ChemDoodle 3D is out.
ChemDoodle® 3D is a molecular modeling and scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.
This is a major update to ChemDoodle 3D a couple of notable features are:
- Major update to the molecular modelling engine. A very accurate implementation of the MMFF94 and MMFF94s force fields can now be used by the Minimizer widget when building molecules.
- You can now set which optimizer function is used, between steepest descent, conjugate gradients and BFGS.
- The Minimizer widget now presents an option to display force field specific atom typing labels for the referenced structure. For the MMFF94 force fields, both the generic Numeric and specific Symbolic atom types are properly attributed in ChemDoodle 3D.
- An advanced system has been added to place new bond connections to atoms in the most optimal location in 3D around the atom. Use this to efficiently create molecules and quickly build coordination complexes.
- A new widget for creating atomic orbital graphics,
- Connolly surfaces and surface colour functions,
- New model types for proteins, including an advanced cylinder and plank model as well as a cartoon model
- Generation of armchair/zigzag/chiral carbon nanotube geometries.
- Significant improvements to the MMTF interpreters, fixing all reported and known issues. Improvements to the CIF interpreters to read a wider range of files. Also fixed a centering issue with CIF input.
I recently wrote a review of Flare Version 2 which is a recent extension to the Cresset portfolio with the introduction of Electrostatic Complementarity (EC), i.e. a comparison of electrostatics on both the small molecule ligand and the target protein. In addition Flare version 2 includes a new Python API, that allows users to automate tasks by scripting, but also integration with other Python packages such as RDKit cheminformatics toolkit, Python modules for graphing, statistics (NumPy, SciPy, MatPlotLib), and Jupyter notebook integration, it is this aspect of Flare that is the subject of this review.
Cresset provide a variety of software packages to support small molecule design, built on the foundation of their extended forcefield XED forcefield. When I first reviewed a couple of Cresset products FieldView, FieldAlign and Forge the forcefield was only applicable to small molecules. However the forcefield has been constantly developed and can now be applied to proteins.
Flare Version 2 is a recent extension to the portfolio with the introduction of Electrostatic Complementarity (EC), i.e. a comparison of electrostatics on both the small molecule ligand and the target protein DOI.
Electrostatic interactions between small molecules and their respective receptors are essential for molecular recognition and are also key contributors to the binding free energy. Assessing the electrostatic match of protein-ligand complexes therefore provides important insights into why ligands bind and what can be changed to improve binding. Ideally, ligand and protein electrostatic potentials at the protein-ligand interaction interface should maximize their complementarity while minimizing desolvation penalties.
In addition Flare version 2 includes a new Python API, that allows users to automate tasks by scripting, but also integration with other Python packages such as RDKit cheminformatics toolkit, and Python modules for graphing, statistics (NumPy, SciPy, MatPlotLib), and Jupyter notebook integration.
Flare gives access to a very powerful set of tools designed to aid ligand binding, docking, electrostatic modelling and WaterSwap, all within a well thought-out interface. The storyboard feature also allows the user to store snapshots of progress and coupled with the log acts like a notebook.
You can read the full review here.
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.
- 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 220.127.116.11. 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.
I just noticed GROMACS 2019 was released on Dec 31 2018.
GROMACS http://www.gromacs.org is one of the major software packages for the simulation of biological macromolecules. It is aimed at performing the simulation of large, biologically relevant systems, with a focus on both being efficient and flexible to allow the research of a number of different systems
Several important performance improvements
- Simulations now automatically run using update groups of atoms whose coordinate updates have only intra-group dependencies. These can include both constraints and virtual sites. This improves performance by eliminating overheads during the update, at no cost.
- Intel integrated GPUs are now supported with OpenCL for offloading non-bonded interactions.
- PME long-ranged interactions can now also run on a single AMD GPU using OpenCL, which means many fewer CPU cores are needed for good performance with such hardware.
In many companies/institutions/universities new arrivals are presented with a variety of desktop tools with little or no advice on how to use them other than "pick it up as you along". This workshop is intended to provide expert tutorials to get you started and show what can be achieved with the software.
The tutorials will be given a series of outstanding experts Christian Lemmen (BioSolveIT), Akos Tarcsay (ChemAxon), Giovanna Tedesco (Cresset), Dan Ormsby (Dotmatics) Greg Landrum (Knime ) and Matt Segall (Optibrium), you will be able to install the software packages on you own laptops together with a license to allow you to use it for a limited period after the event.
Registration and full details are here.
I've mentioned Samson a couple of times and I noticed that the documentation has been updated. Documentation is a critical but often overlooked feature of software.
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
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:
- CppCompilerVersion=5andabove o OpenMP=NO
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.
An interesting recent publication describes pywindow DOI a Python package for the analysis of structural properties of molecular pores (porous organic cages, but also MOFs and metallorganic cages).
Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages.
Freely available on Github https://github.com/JelfsMaterialsGroup/pywindow
Requires numpy, scipy, scikit-learn
A number of Jupyter notebook examples are provided
Example1: Structural analysis of a single molecule loaded from a file type. (multiple examples)
Example2: Structural analysis of a single molecule loaded from an RDKit Molecule object. (required RDKit)
Example3: Calculating an average molecule diameter.
Example4: Analysis of a MOF.
Example5: Analysis of a metal-organic cage.
Example6: Analysis of a periodic system containing several molecular pores that requires unit cell reconstruction.
Example7: Analysis of an MD trajectory containing single molecular pore.
Example8: Analysis of an MD trajectory containing periodic system with multiple molecular pores that requires unit cell reconstruction
Just came across this application and I thought it would be worth flagging, iRASPA is a GPU-accelerated visualization package aimed at material science. Molecular Simulation Journal. 44 (8): 653–676 DOI
iRASPA is a visualization package (with editing capabilities) aimed at material science. Examples of materials are metals, metal-oxides, ceramics, biomaterials, zeolites, clays, and metal-organic frameworks. iRASPA is exclusively for macOS and as such can leverage the latest visualization technologies with stunning performance. iRASPA extensively utilizes GPU computing. For example, void-fractions and surface areas can be computed in a fraction of a second for small/medium structures and in a few seconds for very large unit cells. It can handle large structures (hundreds of thousands of atoms), including ambient occlusion, with high frame rates.
Via iCloud, iRASPA has access to the CoRE Metal-Organic Frameworks database containing 4764 structures and 2932 structures enhance with atomic charges. All the structures can be screened (in real-time) using user-defined predicates. The cloud structures can be queried for surface areas, void fraction, and other pore structure properties.
iRaspa is written in Swift.
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.
Molecular Graphics and Modelling Society Young Modellers’ Forum 2018.
To encourage young molecular modellers at the beginning of their careers, the MGMS invites PhD students who wish to present their work on any aspect of computational chemistry, cheminformatics, or computational biology at the 2018 Young Modellers’ Forum. Other members of the modelling community are are strongly encouraged to attend this event as it is your opportunity to see these talented young modellers and to assist us in the evaluation of the prizes. There is also the chance to discuss the talks afterwards in the pub
Abstract submission 5th October 2018
Date: Friday, 30th November, 2018 Venue: Room QA063, Queen Ann Court, The Old Naval College, Greenwich Location: Details of how to get to the campus can be found at http://www2.gre.ac.uk/about/travel/greenwich.
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
The 2018.01 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a number of new features, enhancements and changes. I written a review that highlights a number of the features.
I've posted about Samson a couple of times and it just keeps getting better and better.
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.
A recent blog post highlights the use of RDKit in Samson.
In this post I will present you the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules from their SMILES code to a 2D and 3D structures. Thanks to the new SAMSON Element, it is now possible to use these features in the SAMSON platform. SMILES code files (.smi) or text files (.txt) containing several SMILES codes can be read using the import button.
The new module allows you to import a file containing SMILES strings, generate 2D depictions, and by right-clicking on these images, you can open, generate the 3D structure in SAMSON or save the image as png or svg.
It is also possible to run substructure searching using SMARTS.
Conformational analysis is a critical component of molecular modelling and I've always viewed OMEGA from OpenEye as the standard to which all other software packages should be compared.
OMEGA's knowledge-based approach produces high-quality conformers, superior to those of many other methods. It has also been found to be the fastest of commercially available conformer generators. Benchmarking Conformer Ensemble Generators, Friedrich, N.-O. de Bruyn Kops, C. Fachsenberg, F. Sommer, K., Rarey, M. Kirchmair, J. J. Chem. Inf. Model. 2017, 57, 2719-2728. DOI.
OMEGA’s capability has been expanded for molecules containing large rings by adding a method specifically tuned to sample macrocyclic conformational space. The approach is based on a rewritten version of the original OMEGA distance geometry algorithm.
In this update support for macOS El Capitan (10.11), macOS Sierra (10.12), and macOS High Sierra (10.13) has been added.
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.
SeeSAR has been updated.
Get fresh inspiration from this huge update of SeeSAR! We realized, on the one hand, that the functionality of the editor was growing and growing, making it more and more complicated to use. On the other hand, access to the full functionality of ReCore demands a different kind of user interface. So we "took the bull by the horns" and, akin to the editor, created the new Inspirator which you can use to do:
- Core replacement This feature is the same but with a much improved UI. You are able to directly select and visualize the bonds that will be clipped to carve out a core fragment for replacement. The clipped bonds now remain in place (even while you define sphere constraints) up until you define a new query. Also the display of results is much enhanced, as you can see the new core fragments highlighted in 2D as well as in 3D. For reference, your query molecule stays visible as well.
- Fragment linking and merging You may of course launch the Inspirator with more than just one molecule. In this case, you can define bonds to clip on different molecules, thereby requesting linker fragments that will connect the remaining pieces. Note that it is not mandatory to clip a terminal part of each molecule to create the query, you may replace a core part in one and connect it to another fragment at the same time.
- Fragment growing This was possibly the most frequently requested functionality in ReCore: Cut just one bond and grow onto this bond using a fragment library of typical side chains. In this way, you can, for example, reach out to nearby subpockets. The new growing algorithm can very quickly scan through a (for now) ready-made library of typical fragments. You may of course define sphere constraints at the same time in order to target particular locations in the bi
You can download SeeSAR here and use it for free for 7 days.
The official release of GROMACS 2018 is now available.
GROMACS is one of the major software packages for the simulation of biological macromolecules.
Highlights from this update include:-
- PME long-ranged interactions can now run on a single GPU, which means many fewer CPU cores are needed for good performance.
Optimized SIMD support for recent CPU architectures: AMD Zen, Intel Skylake-X and Skylake Xeon-SP.
The AWH (Accelerated Weight Histogram) method is now supported, which is an adaptive biasing method used for overcoming free energy barriers and calculating free energies (see http://dx.doi.org/10.1063/1.4890371).
- A new dual-list dynamic-pruning algorithm for the short-ranged interactions, that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall and making runs less sensitive to the choice of the “nslist” parameter.
- A physical validation suite is added, which runs a series of short simulations, to verify the expected statistical properties, e.g. of energy distributions between the simulations, as a sensitive test that the code correctly samples the expected ensemble.
- Conserved quantities are computed and reported for more integration schemes - now including all Berendsen and Parrinello-Rahman schemes.
I see that SeeSAR now supports a parallelized 'real' fragment growing.
SeeSAR is a software tool for interactive, visual compound prioritisation as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximise the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR. Stimulating exploration with SeeSAR, we have embarked on pursuing a new cheminformatics compute paradigm of "Propose & Validate".
You can download SeeSAR here and use it for free for 7 days.
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.
FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).
The Read Me gives download, build and installation instructions, in addition it details how to build the Python interface.
Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189. DOI
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.
SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.
In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make 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
SeeSAR 6.1 has been released, looking at the release notes there are a couple of useful additions.
- Multiple protein alignment, Since version 5.6 it has been possible to load and work with multiple proteins. So far this feature could only be utilized with pre-aligned structures. Now you can do the 3D alignment in SeeSAR itself. The alignment is based on and optimized according to the superposition of related active sites. Therefore, once you have selected a binding site, just one click is all that is needed to superpose all related binding sites at once. Note that the superposition is limited to highly homologous proteins (>90% sequence identity).
- SeeSAR/StarDrop interface. We have implemented a new function that greatly improves the interaction between the two software packages. Using the option in the molecule table toolbar, you may now transfer all (or the subset of favorite) molecules directly to StarDrop, which is launched automatically. This interface is supported in StarDrop starting with the recently released StarDrop version 6.4 and StarDrop now analogously supports launching and submitting data to SeeSAR. So it is in fact possible to transfer data back and forth and exploiting maximum synergy to make the best of both worlds. Note that this feature may require a few adjustments in your SeeSAR settings to become fully functional.
- Shortcut to copy protein ligands. Usually among the first tasks after loading proteins is to copy the related protein ligands to the molecules table for further processing (docking, editing, re-scaffolding, etc.). Especially with multiple proteins this turned out to be a quite cumbersome procedure. Therefore we have implemented a shortcut function in the toolbar of the proteins tab to copy all protein ligands at once to the molecules table. Note that this function will copy all ligands irrespective of their position in relation to the common binding site that is used in the context of the molecules table. So some of the copied ligands may lie well outside the common binding site.
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
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.
It has been a little while but ChemDoodle 3D is out, and looking at the new features it was certainly worth the wait, this is a major upgrade!
New features in ChemDoodle 3D v3:
- Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
- Fully customizable and dynamic real-time shadow rendering.
- Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
- New bond types, more aromatic ring representations, more cheminformatics functions.
- Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
- Fully customizable surfaces can now be built for selections of atoms.
- Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
- Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
- Style sheets (and scene settings files) can now be created, saved and loaded.
- Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
- Full support for the new RCSB MacroZZmolecular Transmission Format.
- A more advanced copy and paste system.
- After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
- Outlines are now rendered for highlighted and selected objects.
- Model settings in the Visuals panel in Preferences are now organized by model type.
- A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
- Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
- Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.
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
- 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:
- 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
- Updated interface to BLOCK 1.0
- 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
- 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
- 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
- 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
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.
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.
The Molecular Design Toolkit is an open source environment that aims to seamlessly integrated molecular simulation, visualization and cloud computing. It offers access to a large and still-growing set of computational modelling methods with a science-focused Python API, that can be easily installed using PIP. It is ideal for building into a Jupyter notebook. The API is designed to handle both small molecules and large bimolecular structures, molecular mechanics and QM calculations.
There are a series of Youtube videos describing some of the functionality in more details, starting with this introduction.
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
- 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
There has been a new update to SeeSAR, this latest update brings.
2D molecule browsing - time to look at things from a different angle
While the molecule table offers great functionality for prioritizing compounds based on the data, it does not provide an overview of the molecules themselves. This release, however, sees the introduction of 2D molecule browsing. The table now offers two views - the one you already know and a 2D browser - flick between them using the switch below the table. Both views are always kept in sync so if you add a filter or sort etc. the 2D browser will show you the same result in the same order as the table. Also try expanding the table area to see how more molecules fit into the view.
Fantastic new 3D graphics features
This release also brings with it some great new 3D graphics improvements. As much as we all like visualising the binding site surface, it lay often times in the way… The binding site surface can now be switched to transparent allowing you to see through it and therefore making the analysis of the binding site and molecules within much more comfortable. Also, the feeling of depth in the 3D view has been improved to help orientation - a so-called "fog effect" fades out the protein and molecules that are further away to bring the foreground more into focus.
Persistent amino acid labels and better view of reference
So far, labels on binding site components unfortunately disappeared when browsing through different molecules in the table. Now amino acid, co-factor and water labels remain present if you change to a different molecule in the 3D view and even if you enter the molecule editor. The view of the reference compound has also been improved. For better visibility, the thickness of the bonds has been increased and instead of coloring the whole molecule in a uniform blue color, only the carbon atoms are colored blue so that hetero atoms can be distinguished more easily.
There is a review of an early version of SeeSAR 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
- 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
A great publication on Open Source Molecular Modeling.
The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.
From toolkits to desktop applications a fantastic and comprehensive listing.
An interesting post on chemistry and computers, Pymol and very large PDB files. The Zika Cryo-EM structure as a case study. Always good to see people stress testing computational tools.
MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach.
Pengfei Li and Kenneth M. Merz, Jr., "MCPB.py: A Python Based Metal Center Parameter Builder." J. Chem. Inf. Model., 2016, Accepted, DOI.
There is an excellent and very detailed online page describing the use of MCPB.py http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm.
BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.
BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.
It can be downloaded from here and requires
- CMake >= 2.8.12
- Python 2.7
- Qt 5.4
Installation instructions for Mac OSX are here
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
SeeSAR Version 4.2 just came out! The main new features are
- You now control when the compute-intense Hyde-calculation runs, this means large sets of molecules can now be loaded, analyzed and processed (e.g. filtering, calculating properties) before the intensive affinity calculations are run.
- Much improved version of grouping all poses of the same molecule
Version 4.2 comes with a load of minor improvements, particularly for the command line use. The full release notes are here.
I've been following this software since it was first released and there is a review here, every update brings useful features. It is well worth downloading the free 1 week trial to have a look at.
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
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.
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.
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.
Chemical Computing Group have just released an up date to MOE, version 2015.10 includes:-
- 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
The PLIP Protein-Ligand Interaction Profiler has been updated.
According to the Changelog
- Support for DNA and RNA as ligands__
- Detection of metal complexes with proteins/ligands, including prediction of geometry__
- Extended result files with detailed information on binding site residues and unpaired atoms__
- Support for zipped and gzipped files__
- Rich verbose mode in command line with information on detected functional groups and interactions
- Automatic fixing of common errors in custom PDB files
- Refined binding site selection
- Better overall performance
- Initial test suite for metal coordination
- Classification of ligands
- Improves detection of aromatic rings and interactions involving aromatic rings
- Single nucleotides and ions not excluded anymore as ligands
- Generation of canonical smiles for complete (composite) ligands
- Generation of txt files is now optional
- Basic support for PDBQT files
- Correct handling of negative chain positions of ligands
- Improved check for valid PDB IDs
- Fixes several bug
The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.
Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.
python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module
All following documentation assumes that you have these installed.
ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge
William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi
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:
- 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
- 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
PDB2PQR 2.0 which is now available from http://www.poissonboltzmann.org/docs/downloads/.
PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES
- Improved look of web interface
- Option to automatically drop water from pdb file before processing.
- Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA.
- Support for compiling with VS2008 in Windows.
- Option to build with debug headers.
- PDB2PKA now detects and reports non Henderson-Hasselbalch behavior.
- PDB2PKA can be instructed whether or not to start from scratch with –pdb2pka-resume
- Can now specify output directory for PDB2PKA.
- Improved error regarding backbone in some cases.
- Changed time format on querystatus page
- Improved error catching on web interface.
OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.
For more information see APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules.
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
a href="http://www.biosolveit.de/SeeSAR/">SeeSAR version 1.6 has been released. It covers:
The ability to change the charge of an Atom (+/-) and to protect such change against ProToss (this is the automated protonation/tautomerism to optimize the overall H-bonding network) overwrite
Improved table: pM affinity, in/exclude multiple columns, the pose-specific context-menu, quick-find molecules including a 2D popup rendering, this can be very useful when trying to work out the structure from a 3D conformation.
A new production release of UCSF Chimera (version 1.10) is available.
Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7.
New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline.
More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
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
You might want to have a look at a new website that I’ve just been sent details of.
CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as JSmol for visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. Below is a partial list of functionality that currently is incorporated into charmming.org:
- A CHARMM tutorial that has been specifically designed for novice CHARMM users
- PDB/CRD reader and input script generator
- Integrated molecular graphics
- Integrated simulation tools (i.e. minimization, solvation, dynamics)
- Automatic topology generation
SeeSAR from BioSolve-it has just been updated, SeeSAR is intended as an interactive tool for designing/improving ligands for drug discovery. This update includes an option to highlight the neighbouring atoms that lead to a particular hyde-score, in the example below the carbon in the ring that gets a pretty big red (unfavourable) score, can be explained by the Receptor desolvation penalty ascribed to the carbonyl oxygen. stereo hardware support (as a first step supporting the polarized-glass-type only), a screen shot feature, an option to move labels out of the way for a better view.
There is a review of SeeSAR here
OEToolkits 2014.Jun This release of the OpenEye toolkits is focused on stability and new platform support. The last release, 2014.Feb, was a major feature release introducing numerous new features. This release focused on fixing many bugs and improving the overall stability of the OpenEye toolkits.
There is still a major new feature being added in this release:
FreeForm API added to Szybki TK
Mac Users should note this release will be the last release to support OSX 10.7.
I recently wrote a review of SeeSAR and one of my comments was:-
Unfortunately there is no 2D display of ligands in the ligand list so sometimes it can be difficult to keep track of modifications.
Well, in keeping with the “fast and agile” release plan a update is now available that includes a 2D display.
SeeSAR is an interesting new product from BioSolve-it, it is intended as an interactive tool for designing/improving ligands for drug discovery. I’ve written a brief review that you can read here.
This is a really interesting application, it seems a little rough around the edges but the developers have released it early are very keen to get feedback. I found them very responsive and enthusiastic about getting the views of users involved in how the application evolves. I would certainly encourage people to download it and use the free trial period to give it a go, and provide them with feedback.
There are more software reviews here.
DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel.
Roberts, Victoria A. and Thompson, Elaine E. and Pique, Michael E. and Perez, Martin S. and Ten Eyck, L. F., (2013) "DOT2: Macromolecular docking with improved biophysical models" Journal of Computational Chemistry, Volume 34, Issue 20, pages 1743-1758, 30 July 2013 DOI:
Version 1.9 of UCSF Chimera has been released.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
This looks to be an extensive update,
New features include
Multiple sequence alignment using Clustal Omega or MUSCLE web services. Building double-helical nucleic acids,"colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options,more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export.
There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.
The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.
More details on the project page
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
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:
- Numpy / Pylab
- Pymol 1.x
- 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
A little while back I posted a comment on the Apple SciTech list asking about options for stereoscopic viewing of molecular modelling on a Mac.
Many thanks to those who contacted me directly, it seems there are a number who have suffered the trials and tribulations of trying to set up stereo viewing. I suspect the combination of different graphics cards, driver, emitters, special connectors, special glasses, program software, X11, operating system changes means that this is a real pain to coordinate support., something always seems to get "updated" breaking everything else.
Which is why this email from Stephan Keith caught my eye.
Let me tell you my solution. It is not necessarily cheaper, but for me, a whole lot easier. I am a 3D software engineer, but I am seriously interested in stereoscopic 3D. I program in C, OpenGL and GLUT. I became weary of all the glasses, buffers, nVidia cards that didn't really work, emitters ... the whole mess. What I do, now, is I write my OpenGL software to create a sidexside or top over bottom stereo display that takes up the entire screen. I then connect an HDMI connector to my LG Stereo 3D Television. I turn on the Stereo3D, put on my RealD glasses. The S3D is passive, not active, so I don't get the annoying flicker, and I don't have to worry about nVidia 3D glasses running out of power (most annoying, at what was $185 a pop). No special glasses, no emitters, no special code, no special connectors. All .... Gone.
I thought I’d try this out, so armed with a copy of MOE a MacBook Pro and a mini display port to HDMI cable I headed down to PCWorld in Cambridge to try it out (many thanks to the people at PCWorld who were really helpful).
I first tried out an LG ELECTRONICS 27MT93V LG MT93V . The first thing I’d say is that the set up was trivial, from connection to viewing a protein in 3D was only a couple of clicks. This gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent. However I found that it was necessary to sit facing absolutely in the centre of the screen to get a good display, also if you move close to the screen then the 3D effect is lost and you get jagged line artefacts. This might not be an issue for a TV but if you paln to use it as a computer monitor I suspect it might be a deal-breaker. I suspect it would be difficult to sit alongside colleagues and have them all have a good 3D impression.
I then tried an active 3D display on a Samsung UE46F6800 46-inch Widescreen TV, this was much larger than I needed but I understand there are smaller models available. Once again setup was a breeze, this gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent, and the brightness did not seem to be impacted at all by the active glasses. The 3D viewing was acceptable at a wide range of screen angles and distances and it should be possible to sit beside colleagues to discuss a project and all have a good 3D view.
I wear prescription glasses and I found the active glasses fitted comfortably over my glasses. They were also a lot more lightweight than I remember in the past. In the past active shutter glasses have been very expensive but prices have dropped significantly.
Personally I found the Active 3D much superior, especially if you planning to use this mainly as a computer monitor rather than a TV that you view from the comfort of your sofa.
Whilst the update to PYMOL was announced as part of the Schrodinger update I thought it deserved a separate blog entry.
- Greater user control over color settings ◦ Color settings can be set as hexadecimal, colors, or floats ( [1., 1., 1.])
- New ‘focalblur’ command
New ‘callouts’ for scene annotations
Improved and extended Filter Wizard
- New commands ◦ Retrieve bond properties with get_bond ◦ Load structures from PubChem by SID and CID codes with fetch
- Improved PDB Loader graphical interface
- Expanded documentation of settings
- Access settings and properties from the iterate/alter commands via “s.” and “p.”
- Improved labels to include customizable connectors to atoms, multiline labels, and more
- Ability to select atoms by coordinates or by user-defined property
- New selection keywords: metals, sidechain, backbone
CTRL-F to find objects or selections in the Object Menu Panel
Dynamic measures now stored in session files
- Sequence viewer colors fixed
- Fixed inversion problem with ‘cealign’
Improved stability for shader-based rendering
New option to embed content within a PowerPoint file
- Support PowerPoint PPTX file format
- Improved installer
- AxPyMOL control displayed as an “Add In” on the PowerPoint Ribbon
- 32-bit and 64-bit Office Support
- Embeddable presentation content
- Initial support for MAE files
- Shader-based rendering support for volumes and improved graphics
- Many bug fixes
The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.
In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months
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 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)
Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs
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
Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)
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
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
In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.
While this is useful if you have similar structures (perhaps analogues in a series) there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this.
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 was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.
MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview.
Sure enough the update on Dec 24th has this in the release notes.
Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.
There are a number of suitable glasses on Amazon 3D Red/Cyan Glasses
I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.
For science apps for iOS have a look at the mobile science page.
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.
- 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.
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.
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.
Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).
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.
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.
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.
Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.
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.
One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.
The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.
The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.
It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.