Macs in Chemistry

Insanely great science

Mac OS X Applications D-I

Dalton :- Molecular electronic structure

Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
  • First- and second-order methods for geometry optimizations
  • Robust second-order methods for locating transition states
  • Constrained geometry optimizations; bonds, angles and dihedral angles can be fixed during optimizations
  • General numerical derivatives that automatically makes use of the highest order analytical derivative available
  • HF and DFT code direct and parallel using replication of Fock matrices using either MPI or PVM3 for message passing
  • Effective core-potentials (ECPs)

Data Desk :- Data analysis and visualisation

  • Data Desk's dynamic plots and tables show patterns and structure among several variables. Rotating plots and sliders use animation to reveal aspects of your data that static plots cannot show. Changing the color, symbol and selection state of datapoints instantly changes all plots to show patterns, clusters, and outliers. Hot Set selections restrict displays to subsets of your data with a single click.

DataGraph:- 2D data analysis and plotting

At the recent WWDC 2006 there was a discussion about the need for a simple 2D plotting tool, to meet this need David Adalsteinsson the author of the scientific visualisation tool DataTank has created DataGraph (formally known as DataPlot) a great new 2D plotting tool with the design philosophy "Simple and Powerful Plotting". I've written a review for MacResearch and you can read a copy here.

A DataGraph.framework can be downloaded here. This allows you to use DataGraph as a graphing engine in your own program. This is works independent of DataGraph, but you need a license in order to make use of it.

DataTank :- Data analysis and visualisation

DataTank is designed for scientific visualization, data mining and algorithm development, but it is flexible enough to be used for a variety of other uses as well. DataTank enables interactive exploration of large data sets. Variables and relationships are defined graphically and built in modules can be combined with your own modules. DataTank will manage memory and perform incremental evaluation, treating data sets with millions of data points and hundreds of thousands of entries the same way as a simple data set that is typed in manually. To make this possible DataTank uses caching extensively, both in memory and on disk..

Daylight :- High performance cheminformatics toolkit

Daylight The Daylight toolkit and high performance cheminformatics database have been ported to MacOSX and is now available. The Daylight Toolkit is a programming library that provides all functions needed for chemical information processing and substructure pattern searching along with fingerprinting and similarity capabilities.

DelPhi:- Solves Poisson_Boltzmann equation

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions.
Runs on Macintosh. Executable is also provided.The PowerPC Mac executable version of delphi is dynamically linked to IBM XL compiler libraries. It will not run unless you have these libraries on your local system. Intel Mac version - runs on Macintosh with Intel processor. Executable is also provided.

Dilutions:- iPhone app that helps perform Serial Dilutions and make SDS-PAGE gel

Dilutions contains several calculators that help perform Serial Dilutions and make SDS-PAGE gel: Serial Dilutions - calculates initial amounts of stock and media along with the transfer volume in the serial

DINO :- Molecular visualisation

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines).

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

Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
The DIRAC program computes molecular properties using relativistic quantum chemical methods.
New features in [DIRAC12](http://diracprogram.org/features/) (released 12/12/12)

* 2-component relativistic Effective Core Potentials (ECPs)
* London Atomic Orbitals (LAOs) at the DFT level
* Simple magnetic balance for NMR shieldings
* LAO current densities
* Overlap diagnostic for TD-DFT calculations of excitation energies
* Pipek-Mezey localization by trust-region optimization
* Long-range MP2/short-range DFT
* Atomic start guess for SCF calculations
* MP2 natural orbitals
* Complex/Damped DFT response module
* New Lanczos algorithm for relativistic Algebraic Diagrammatic Construction (ADC)
New features in DIRAC10 (released 10/10/10)
* Methods:
* Kramers-restricted MCSCF
* RELADC for correlated calculations of single/double ionization spectra
* large-scale parallel CI (LUCITA/KRCI)
* intermediate Hamiltonian formalism for Fock-space CCSD
* interface to MRCC (see http://tc03.fkt.bme.hu/)
* frozen density embedding
* Hamiltonians:
* 2c X2C+AMFI for 2-electron spin-orbit corrections (spin-same orbit[SSO]/spin other-orbit[SOO])
* Molecular properties:
* HF/KS excitation energies
* KS response with noncollinear spin polarization and full derivative of functionals
* linear response functions at imaginary frequencies
* more efficient KS DFT code
* London orbitals for HF NMR shieldings
* Analysis:
* visualization of unperturbed and perturbed densities
* projection analysis of expectation values
* expectation values/transition moments KRCI/GOSCI
Features in DIRAC08
* Methods available:
* Hartree-Fock
* Density Functional Theory
* Coupled Cluster
* Configuration Interaction
* Møller-Plesset Perturbation Theory
* Hamiltonians available:
* 4c Dirac-Coulomb (includes scalar relativistic effects and spin-own-orbit coupling)
* 4c Dirac-Coulomb-Gaunt (includes also spin-other-orbit coupling) (only HF)
* 4c spin-free Dirac-Coulomb (scalar relativistic effects only)
* 4c Levy-Leblond (nonrelativistic)
* 2c X2C, the one-step exact two-component Hamiltonian
* 2c BSS, the two-step exact two-component Hamiltonian (= DKH(infinity,0))
* Molecular properties:
* Up to quadratic response properties at the Hartree-Fock and DFT level
* First order properties with MP2
* Core excitation energies in the static exchange (STEX) approximation.
* Single/Double Ionization energies and spectra at the ADC(3)/ADC(2x) level of theory.
* Efficiency:
* Full symmetry handling for linear molecules (otherwise up to D2h)
* Parallelization using MPI library calls (MPI should be preinstalled)
* Some of the new features of DIRAC08:
* A one-step exact two-component Hamiltonian (X2C)
* Relativistic Green's function (propagator) module RELADC for the calculation of ionization energies
* Possibility to include the Gaunt interaction in HF calculations
* Implementation of several new density functionals
* Linear and quadratic response DFT
* Addition of the latest Dyall basis sets and more non-relativistic basis sets to the basis library
* Analysis by means of fragment orbitals
* New parallelization of the MOLTRA module with reduced I/O
* Parallelization of the LUCITA CI module

DiscoveryGate :-Online searching

Fully Tiger compatible, DiscoveryGate from MDL offers scientists broader access to a structure-searchable online platform for integrated researching of databases, journal articles, patent publications and reference works.

Distillation Designer:- McCabe-Thiele method for designing binary distillation systems.

Distillation Designer provides the simple McCabe-Thiele method for designing binary distillation systems.

Supports:
  • Boiling Point Graph showing Vapour-Liquid Compositions.
  • q-Line calculation from component thermodynamic properties.
  • Manually defining the minimum reflux ratio.
  • Loading of Data files.
  • Plot of Reflux versus stages to help determine the optimal value.
  • Drag and Drop graphs direct to desktop.
  • Configurable printing of the 3 Graphs
  • Much better checking of input data before the McCabe-Thiele graph can be plotted.

DivCon MOE GUI

MOE/DivCon GUI is an integration interface that joins the QBLib with the powerful Molecular Operating Environment (MOE) from the Chemical Computing Group (CCG), creating a technological innovation for protein/ligand scoring (energetically favorable), featuring QM, PWD, and NMR Scores.
The integration provides a unique tool for accuarate quantum mechanical data to be calculated using QuantumBio's proprietary toolkit and visually displayed through the MOE database. Obtained data from the MOE/DivCon GUI is comparative to other techniques users accomplish in MOE. QuantumBio's interface makes setting up calculations easy and straightforward.
surfaceribbonpoly

DiversityGenie:- Analysis of sets of organic compunds

 

Diversity Genie is a small but powerful utility to analyze datasets of small organic molecules. Its features include:

Calculation and comparison of diversity of chemical sets* Ability to handle sets of millions of molecules Sorting, slicing, and merging large SD files Conversion between SMILES, InChI, and SDF formats Filtering based on property values and structural uniqueness Computation of 2D and 3D atomic coordinates Addition/Removal of implicit hydrogens Computation of molecular properties such as molecular weight, number of rotatable bonds, number of HBO, HBA, as well as other descriptors Export and import of data to/from CSV files Data visualization

DL Visualize:- visualisation of materials structures and properties

DL Visualize is a new, state-of-the-art package for the visualisation of materials structures and properties
beta port to Mac OS X (uses Darwin Unix OS core).

DOCK:- Docking tool

DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

DOT 2.0:- Macromolecular Docking Software

 

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:

DRAWxtl:- Crystal structure display

The purpose of DRAWxtl is to display crystal structures on ordinary computer hardware and operating systems. Four forms of graphics are produced: (1) an openGL window for immediate viewing, (2) the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings, (3) the Virtual Reality Modeling Language (VRML) for dissemination across the Internet, and (4) a Postscript rendering of the OpenGL window for those that want high-quality output but do not have POV-RAY installed.

EasyChem :-Structure drawing

The open source EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.

eBioTools:- a compilation of bioinformatics software

eBioTools is a compilation of bioinformatics software that has been packaged for easy installation on Mac OS X. It covers many areas, from simple sequence analysis to RNA folding and sequence assembly.
The included programs can be run from the command line in the Terminal program. If you are interested in something that is more easy to use, please take a look at our program eBioX, which works as a graphical interface for eBioTools.

eBioX:- GUI for EBioTools

eBioX brings easy-to-use sequence analysis to Mac-using biologists. It features an editor for sequences and multiple alignments, and graphical viewers for trace files and molecule structures. Many popular file formats are supported. Databases can be created locally or queried over the network, both for metadata and homology (BLAST). Analysis functions include searching for patterns, primers, restriction sites and repeats, translation and back translation, calculating DNA melting temperature, dot plots, as well as aligning sequences (multiple, local and global). Multiple alignments can be created by several of the most popular algorithms

Eden :- Electron density

Eden is crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner. This program improves macromolecular crystallographic electron density maps in a maximally unbiased manner. There are now two versions of eden, "seden" and "deden." seden is compiled with single-precision fftw libs, and is faster and less memory-intensive. deden is double- precision and is possibly more accurate (but in practice the differences appear insignificant). ieden is a new python Tkinter-based GUI. Type "eden" or "seden" to invoke single-precision eden, "ieden" for the GUI, and "deden" for double-precision eden. GUI users need to define the environment variable EDITOR, eg: export EDITOR='see' or setenv EDITOR vim.


Elemental:- Chemical Drawing

Elemental is written in javascript and so there is no java security dialog, it also loads very quickly. The interface is clean and uncluttered with all the regularly used functions visible.
Use templates of common substructures to build complex compounds more quickly
Add user defined substructures to the list of templates to create compounds of similar structure
Export created molecules as mol files to other applications
Violations of allowed valence are automatically flagged up
Flexibility to select any element from the periodic table
Build reactions using the drawing tool.
elemental

There is a brief review of
Elemental here.

EleMints:- iPhone periodic table

EleMints is a totally interactive Periodic Table for the iPhone and iPod Touch. However, it not only offers a Periodic Table, but also a Plot Graph, Element listing, Molar Mass
Calculator, and more.

eFindSite:-Binding site prediction

eFindSite is a ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins and is described in detail in a recent publication. Brylinski M, Feinstein WP.  2013.  eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des. 27(6):551-567 DOI It employs a collection of effective algorithms, including highly sensitive meta-threading approaches, improved clustering techniques, advanced machine learning methods and reliable confidence estimation systems.

Detailed compilation instructions for Mac OS X are here.


EnCIFer:- validate CIF files

 

The Crystallographic Information File (CIF) is the internationally agreed standard file format for information exchange in crystallography. The CIF standard is supported, maintained and developed by the International Union of Crystallography (IUCr) and most major journals require electronic data depositions in CIF format. enCIFer enables users to validate CIFs and ensure their files are format-compliant for deposition with journals and databases or for storage in laboratory archives. enCIFer should also be used to add information safely to CIFs without corrupting the strict syntax. enCIFer operates on single or multi-block CIFs allowing you to:

  • Identify and correct syntax/format violations
  • Safely edit information to your CIF without corrupting the strict syntax, for both single data items and data loops
  • Supplement the data in your CIF via two data entry wizards, one for publication details and the other for chemical, physical and crystallographic properties
  • Select from a choice of CIF dictionaries and check against a user-customisable list of mandatory data items
  • Visualise structure(s) in a CIF, including displacement ellipsoids

Requires Mac OS X: 10.6, 10.7, 10.8, 10.9

EON :- Compare molecular electrostatics

EON is an electrostatics comparison program - it compares electrostatic potential maps of aligned molecules and determines the Tanimoto measures for the comparison. Thus databases of molecules can be screened for electrostatic similarity to a lead compound. Since the input molecules must already be aligned, EON is suitable for analyzing the output structures from programs such as ROCS, thus yielding compounds with similar shape and electrostatics. EON should contribute significantly to lead generation and library desigm.

European Molecular Biology Open Software Suite (EMBOSS)

EMBOSS the European Molecular Biology Open Software Suite is a package of over 100 high-quality FREE Open Source software for sequence analysis.

EMAN :-Reconstruct 3D images from EM-pics

EMAN is a software to reconstruct 3D images from EM-pics. There are also a number of other structural biology applications available here

Evince :-Data analysis

Evince newly developed java based platform for advanced data analysis. The software can be used for design of compound libraries and contains a combination of multivariate statistical algorithms such as PCA and PLS and interactive visualisations. For example can data be imported in .sdf format and molecule structures shown in 3D together with results from multivariate modelling.

Facio:- free GUI for computational chemistry softwares

 

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

cubemo_w_m


FAF-Drugs2:- This is a package for in silico ADMET filtering

FAF-Drugs2 (Free ADME-Tox Filtering version 2) is a program for filtering large compound libraries prior to in silico screening experiments or related modeling studies. The main goal is the computational prediction of some ADME-Tox properties (Adsorption, Distribution, Metabolism, Excretion and Toxicity)1. Additionnaly without managing a whole filtering process, FAFDrugs2 has basic capabilities as removing salts and conterions, removing duplicates or computing the ADMETox descriptors without filtering the database

Fconv:- Molecular file manipulations

  • Fconv is a command-line tool for several tasks concerning manipulating, converting, and analyzing data from different file formats.
  • - Convert pdb to mol2 files
    - Extract ligands from pdb files as mol2 files
    - Correct errors in pdb files
    - Reset atom types to many different atom type definitions (e.g. TRIPOS / SYBYL)
    - Add missing hydrogens
    - Merge or split multimol2 files
    - Build the unit cell for a crystal structure
    - Calculate the number of freely rotatable bonds, molecular weights, exact RMSD values, and other properties
    - Convert Autodock dlg files to mol2 files (with or without reference)
    - Convert sdf files to mol2 files
    - Convert cif files to mol2 files
    - Substructure searches

FieldAlign :- Align electrostatic fields

FieldAlign is a powerful design and 3D Structure Activity Relationship (SAR) tool for Computational and Medicinal Chemists that shows where active compounds are similar and how they differ. Given the 3D structure of an active molecule and a series of 2D compounds (pasted or imported from your favorite drawing package), FieldAlign will compare the molecules’ Fields to generate the best 3D alignment for your compounds. FieldAlign enables Computational Chemists to:
  • Increase their understanding of where and how their lead molecules bind to their protein targets
  • Perfect the design of new lead compounds, exploring a range of lead optimization ideas
  • Prioritize syntheses and reduce time by avoiding making dead-end or uninformative compounds
  • Optimize the design of a focused library for synthesis or initial screening
  • Screen small libraries of compounds looking for a backup series with more structural diversity
Every alignment is scored and ranked so you can see the highest scoring compounds with the most similar activity and properties at the top of the list. These can also be viewed in 3D alongside your target active molecule allowing you to gain full understanding of how your molecules interact with the protein.
fieldalign_example

There is a
review of FieldAlign here

FieldTemplater :- Pharmacophore generator

Working from just a few 2D structures of known active ligands, FieldTemplater generates a series of conformations that the ligands might adopt at physiological conditions. It analyzes these conformations to find sets that show a high molecular Field similarity (and hence have similar shape/binding properties).Where all the ligands with a common activity align well, it is very likely that this is the bioactive conformation. The similarities and differences in the sets provide insights into how active ligands bind to a common active site.
fieldtemplater_example

FieldView:- View molecular electrostatics

FieldView enables you to load your structures from SDF and MOL2 files as well as showing results from all Cresset applications. You can import and compare up to 10,000 compounds at once or copy and paste them into FieldView from your favourite drawing package.
Using FieldView you will be able to:
  • Create and modify structures using the in-built molecular editor
  • Automatically convert structures from 2D to a minimized 3D conformation
  • Clone and compare molecules side by side or overlaid using Cresset’s unique Field technology
  • Understand how a compound’s activity, ADME and toxicity properties vary with their molecular Fields
  • View virtual screening results, such as those from FieldScreen, comparing 2D structures with a 3D overlay showing all the Fields of every ligand
  • Filter molecules based on the exact mix of properties you need

There is a
review of FieldView here

FileMaker :- Powerful and easy to build Database

  • If you need to build a custom database but don't want the overhead of learning SQL then you should seriously look at FileMaker. Many custom solutions are available and the built in scripting language allows you to build very sophisticated solutions easily.

Filter:- Rapid filtering of structures

FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.

Fitted:- Flexible molecular docking

FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds with the protein side-chains.

  • FITTED is a suite of programs (FITTED, ProCESS and SMART)
  • Fully automated and flexible docking program
  • Uses an evolutionary algorithm
  • Semi-flexible protein docking with flexible waters
  • Has the ability to consider water molecules displaceable
  • Different docking modes available: Dock, Filter, SAR, VS and Score
  • Runs on Linux, Mac and Windows
  • Accuracy and speed

Filter-it:- molecule filter

Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.

fityx:-

fityx is primarily used...
  • by scientists who analyse data from powder diffraction, chromatography, photoluminescence and photoelectron spectroscopy, infrared and Raman spectroscopy, and other experimental techniques,
  • to fit peaks – bell-shaped functions (Gaussian, Lorentzian, Voigt, Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic, etc.),

Firefly:- a freely available ab initio and DFT computational chemistry program

Firefly (previously known as the PC GAMESS) is a freely available ab initio and DFT computational chemistry program developed to offer high performance on Intel-compatible x86, AMD64, and EM64T processors. Firefly package is being developed by the Firefly Project Team.

The Mac OSX version can be downloaded here together with installation notes and user and quick start guides.

Details of this major update can be found on the news page


Folding@Home :- Protein folding

Folding@Home is a distributed computing project looking at protein folding -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world.

Force Field Explorer:- Graphical user interface to TINKER

Force Field Explorer is a graphical user interface to the TINKER suite of molecular modeling tools

FORECASTER :- Includes programs for drug discovery and process chemistry

I just heard about a platform - FORECASTER - that includes programs for drug discovery and process chemistry, these include

1. FITTED, a docking program
2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
3. CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
4. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
5. REDUCE, a program that filters using descriptors and functionnal groups
6. REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
7. IMPACTS, a sites of metabolism prediction program (CYP 450)
8. ACE, a program that predicts the stereochemical outcome of reactions

All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows. 

You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery

ForgeV10:- SAR analysis and ligand design

forgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint

It is designed to

  • Decipher complex SAR and communicate the results
  • Design better molecules based on predictions you can trust
  • Prepare detailed pharmacophores
  • Virtually screen 10 000 compounds on your desktop
  • Generate ADME and off target activity profiles.

FOX:- ab initio structure determination from powder diffraction

The FOX program (for Linux, MacOS X and windows) was made for the ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are:
  • a versatile description of the crystal contents: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions..
  • an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms.
  • the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern)
  • smart global optimization algorithms which can get out of false minima.

FRED :- Molecular docking

Based on an original scientific perspective and efficient computational algorithms,FRED is an accurate and extremely fast docking program. With equivalent resolution settings, FRED will out-perform all known docking programs, typically examining about a dozen ligand conformers in a second. For each, FRED exhaustively examines all possible poses within the protein active site, filtering for shape complementarity and pharmacophoric features before scoring with more traditional functions.

FreeSASA: _An open source C library for solvent accessible surface area calculations

 

Calculating solvent accessible surface area is an important calculation in the study of protein structure and whilst there are many tools to undertake this sort of calculation FreeSASA represents the first open-source free standing tool for this sort of calculation. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces.

Source code is available for download here and building the FreeSASA library and command-line interface only requires standard C and GNU libraries and a C99-compliant compiler, and should be straightforward on any UNIX system (has been tested in Mac OS X 10.8 and Debian 8).

Mitternacht S. FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: awaiting peer review]. F1000Research 2016, 5:189 DOI


Gabedit:-Graphical user interface to computational chemistry package

Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess and Q-Chem
It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.
Major features
  • Gabedit can Creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, PCGamess and Q-Chem.
  • Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess, Q-Chem and (partially) ADF calculation results, including the following
    • Molecular orbitals.
    • Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
    • Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property.
    • Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the principal axes of the molecule.
    • Animation of the normal modes corresponding to vibrational frequencies.
    • Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the principal axes of the molecule.
    • Animation of contours, Animation of planes colorcoded.
  • Gabedit can display UV-Vis, IR and Raman computed spectra.
  • Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded.
  • Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
  • Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded).
  • Simulated Annealing with Molecular Dynamics is implemented in Gabedit (using Amber 99 molecular mechanics parameters).
  • It works under Windows, Linux, Mac OSX11 and other UNIX OS. 
Computational chemistry packages supported ( (to date) by Gabedit are : Gamess-US , Gaussian  , Molcas , Molpro , MPQC , OpenMopac , ORCA FireFly  and Q-Chem  . ADF, Turbomole, and other softwares (through the gabedit and molden format files)  are partially supported by Gabedit.

GAMESS :- Ab Initio

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order Perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment Potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including third order Douglas-Kroll scalar corrections, and various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments.
A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials, so all elements up to Radon may be included in molecules. Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolPlt program for the Macintosh, are available for viewing of the final results.

GamessQ:- A companion to GAMESS and MacMolPlt

Very simply gamessQ provides a queueing functionality for GAMESS computations running on your local desktop/laptop. gamessQ is a gui application and provides drag and drop fucntionality for running jobs with gamess that would otherwise require the use of the command line.

GAMGI:- Molecule Viewer

GAMGI aims to be useful for: 1) the scientific community working in atomistic modelling, who needs a graphic interface to build and analyse atomic structures; 2) the scientific community at large, who needs a graphic interface to study atomic structures and to prepare images for presentation

GAMMA:- NMR C++ library

GAMMA is a C++ library expressly for simulation of Magnetic Resonance experiments. It was written by Scott A. Smith and Tilo Levante under the guideance of B.H. Meier and R.R. Ernst at the ETH in Zürich, as described in the article


"Computer Simulations in Magnetic Resonance.
An Object Oriented Programming Approach",
S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst,
J. Magn. Reson., 106a,

Gaussian 09M :- Ab initio Structural Modelling

Gaussian 09M is a complete implementation of the popular Gaussian electronic structure modeling program for the Mac OS X environment. Also GaussView a full featured graphical user interface is now available for MacOSX.

GaussView:- Gaussian viewer

GaussView is the most advanced and powerful graphical interface available for Gaussian. With GaussView, you can import or build the molecular structures that interest you, set up, launch, monitor and control Gaussian calculations, and retrieve and view the results, all without ever leaving the application. GaussView 5 includes many new features designed to make working with large systems of chemical interest convenient and straightforward. It also provides full support for all of the new modeling methods and features in Gaussian 09. This brief introduction will give you a Quick Start to using GaussView 5 to investigate molecules and reactions with Gaussian 09.
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GDIS :- Molecular Display

GDIS is a GTK based program for the display and manipulation of isolated molecules and periodic systems. It is in development, but is nonetheless quite functional. It has the following features:
  • Support for many common file formats (eg CIF, PDB, XTL, XYZ).
  • OpenGL rendering.
  • Assorted tools for visualization (measurements, ribbons, polyhedral display).
  • Useful manipulation tools, including matrix transformations and supercell construction.
  • Powerful surface generation and crystal morphology tools.
  • Diffraction pattern generation and plotting.
  • Animation and movie generation for multi-frame files.
  • Analysis of Molecular Dynamics simulations.

GenomeBrowse

 

GenomeBrowse focuses on displaying data in a form that helps you quickly and easily understand what the data is saying. Each variant and its surrounding context is displayed in extraordinary detail. To help you get the most out of your data, GenomeBrowse provides:

  • * Multiple coverage and pile-up views that make mismatches stand out.
  • * Natural pan and zoom controls that quickly allow you to zero in on a region of interest.
  • * Stacking algorithms that provide stable pile-ups so that your genomic context is constant.
  • * Customizable color palettes to tailor plots to your data.
  • * A smart labeling system that balances clarity with information density.
  • * Integrated search and location bar.
  • * External links to UCSC, Ensembl and NCBI.
  • * Multiple views of the same data source: Feature tables, per-click feature report, multiple plot types per source.
  • * Plots that are easily customized with on-plot hover controls and advanced options in a plot-type specific control panel including styling, smoothing, and filtering.

Ghemical :- Molecular modelling

Ghemical is a computational chemistry software package released under GNU GPL. Requires X11.

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

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

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

GTKDynamo:- Molecular modeling extension for PyMOL

 

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

Some capabilities include:

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

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

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

GTKDynamo_overview-page001_800

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

Graphite - LifeExplorer: Protein/DNA modeling

Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.

You can see a it in action here

http://www.youtube.com/watch?feature=player_embedded&v=9db1hXZARoo

GridChem client:- Desktop client for Computational Chemistry Grid

The "Computational Chemistry Grid" (CCG) is a virtual organization that provides access to high performance computing resources for computational chemistry with distributed support and services, intuitive interfaces and measurable quality of service. The CCG client, GridChem, is a Java desktop application that provides an interface to integrate the hardware, software and middleware resources necessary to solve quantum chemistry problems using grid technologies.

GROMACS :- Molecular dynamics

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. See also Tips to compile gromacs on MacOSX or download a binary here

GSAS :- Solid and Powder diffraction analysis

GSAS is a set of programs for the processing and analysis of both single crystal and powder diffraction data obtained with x-rays or neutrons. It is capable of handling all of these types of data simultaneously for a given structural problem. In addition, it can handle powder diffraction data from a mixture of phases refining structural parameters for each phase.

GULP :- Solid and Polymer modelling

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

Scientific details about GULP can be found in the following papers:
1. GULP - a computer program for the symmetry adapted simulation of solids, J.D. Gale, JCS Faraday Trans., 93, 629 (1997)
2. Empirical potential derivation for ionic materials, J.D. Gale, Phil. Mag. B, 73, 3, (1996)
3. The General Utility Lattice Program, J.D. Gale and A.L. Rohl, Mol. Simul., 29, 291 (2003)

HADDOCK :- Molecular Docking

High Ambiguity Driven biomolecular DOCKing (HADDOCK).
HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process.

The concept of HADDOCK is described in the following paper:


Hibridon:- Solve inelastic collisions.

Hibridon, a program package to solve the close-coupled equations which occur in the quantum treatment of inelastic atomic and molecular collisions. Gas-phase scattering, photodissociation, collisions of atoms and/or molecules with flat surfaces, and bound states of weakly-bound complexes can be treated.

HKL-2000 :- Structural Biology

HKL-2000, a new program package based on the original HKL Suite, is the premier software of choice for structural biology. Analysis of the Protein Data Bank (PDB) shows that nearly 80% of all entries were processed with the HKL/HKL-2000 package and it is now available for MacOSX.

Hybrid:- Ligand guided docking

HYBRID is a docking program that can utilize bound ligand information in a seamless manner. Like FRED, HYBRID performs a systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site; however, instead of filtering the poses based on their shape complementarity to the active site, they are filtered on their shape and chemical complementarity to a known bound ligand.

HyperChem :- Molecular modelling

HyperChem is now available for MacOSX, OpenGL graphics for sophisticated rendering of molecules and properties, Full range of molecular mechanics and quantum mechanics methods., Protein and DNA capabilities for modeling and manipulation with PDB files. Scripting capabilities to automate and your molecular modeling workflow.Molecular dynamics, Langevin dynamics and Monte Carlo statistical mechanics. Spectral computations including vibrational analysis and excited electronic states.

iBabel :- Molecular file conversion and viewer

iBabel is an AppleScript Studio application that provides a graphical interface for the command line-driven file conversion application OpenBabel. The update requires the installation of OpenBabel 2.0, and includes additional file conversions as well as very fast similarity and sub-structure based searching. Structures can be viewed in 2D or 3D as appropriate using the embedded Jmol or JChempaint applets. Now uses ChemSpotlight to search chemical content on your hard drive.
Version 3.0 of iBabel is now in beta testing.

ICEDIT:- Chemical drawing java applet

ICEDIT is the new chemical structure- and reaction-editing tool developed at InfoChem following customer-specific requirements. Features such as:

  • easy integration in any desktop or web application

  • advanced options for the definition of query features

  • support of complex R-group query specification


  • Supported Browsers: Internet Explorer 5.5 or higher, Firefox (Windows, Mac OS X, Linux), Opera, Netscape, Safari (Mac OS X)

  • Software: Java Runtime Environment JRE 1.1.x or higher


iChem :- Periodic table

iChem written in Cocoa for Mac OS X exclusively, iChem is a full-featured periodic table and molecular weight calculator.

iChemistry:- iPhone equation balancer

iChemistry: Chemical Equation Balancer and Stoichiometry Calculator

ICM-Modules :- Biology and Chemistry

ICM from molsoft stands for Internal Coordinate Mechanics and was first designed and built to predict low energy conformations of biomolecules. ICM also is a programming environment for various tasks in computational structural biology, sequence analysis and rational drug design.

ICM is distributed in the following packages:

  • ICM-browser and ICM-browser-pro (distributed from a single package)
  • ICM-chemist and ICM-chemist-pro (distributed from a single package)
  • ICM-pro with options including bioinformatics, Poisson electrostatics, chemistry and cheminformatics, homology modeling, docking, virtual ligand screening (VLS).

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iCut DNA:- iPhone app to search the Restriction Enzyme Database (REBASE)

iCut DNA lets you search the Restriction Enzyme Database (REBASE) for enzymes and the DNA nucleotide sequences they cleave. You can use it to find commonly used (type II) restriction enzymes by name or by specifying the recognition

IGOR Pro :- Data analysis

IGOR Pro is an interactive environment for experimentation with scientific and engineering data and for the production of publication-quality graphs and page layouts.

iMass :- Molecular mass calculator

iMass a molecular mass calculator, a periodic table of the elements, an isotope distribution graph and a calculator that computes elemental compositions matching a given mass. iMass understands complex chemical formulas as well as user defined abbreviations for commonly used formulas.

iMol :-Molecular viewer

iMol is a free molecular visualisation program written in Object C and using OpenGL for the graphics so no need for X-windows, the author Piotr Rotkiewicz is looking for feedback. Updated May 24 2007.

iMolBuilder:- iPhone application

The iMoleBuilder is an application that can view, edit and build molecules in 3D. Users can easily analyze a molecular structure by rotating, moving, and zooming it.

iMolDraw :- iPhone application for chemical drawing

The iMoleDraw is an application that can view, edit and build molecules in 2D.

InDigestion :- Proteomic tool

InDigestion is a handy Mac OS X application for calculating protein properties used in proteomics. Currently it calculates molecular weights of intact proteins, performs enzymatic digests, and creates hydrophobicity plots. InDigestion is created using the BioCocoa framework.

Indigo:- Cheminformatics Toolkit

  • Indigo is an organic chemistry toolkit. The code base is shared among the projects. All of the tools are written in C++, while a number of C# and Java wrappers are available.
  • Bingo: Cartridge for Oracle database supporting a wide range of searches in organic chemistry databases. Absolute portability, great scalability, plus unique features like:

    • Resonance substructure search

    • Tautomer substructure search with user-defined rules

    • Canonical (absolute) SMILES computation

    • Fast table update with no need to rebuild the index

    • Multi-threaded table indexing

  • Dingo: Molecule and reaction rendering library with C# wrapper and command-line utility. Best picture quality among all available products. Excellent portability. Easy SVG support. Automatic layout for SMILES-represented molecules and reactions.

  • Cano: Canonical SMILES computation library with C# wrapper. Unique support of tetrahedral and cis-trans stereochemistry features.

  • Deco: R-Group deconvolution and scaffold detection library and command-line utility. Pioneer work in computing the exact maximum common substructure of arbitrary amount of input structures.

  • Nucleo: Nucleotide chain handling library with Java wrapper. Includes canonical SMILES computation.

InforSense KDE :- Data analysis

InforSense KDE is an Integrative Analytics platform used for seamless integration of all data types, for improved decision-making across life sciences research. BioSense Grid adds a service-based high-performance environment for creating bioinformatics applications

iNMR :-NMR analysis

iNMR is now a universal binary, the only NMR tool designed specifically for the Mac. This fantastic tool for the processing and analysis of NMR data in a Mac environment has beeen updated to version 2.2.22. It can import SwaN-MR, JCAMP-DX, Bruker (Aspect, Win-NMR, XWin-NMR, TopSpin), Varian, SpinSight, Tecmag, Jeol Delta, GE Medical, Siemens. Other formats can be converted indirectly, via SwaN-MR or Jeol Delta. Other importing filters can be added at no additional cost. iNMR is a product by nucleomatica.
The website also includes a wealth of information including
tutorials and visual guides

Instant JChem:- Desktop Chemistry Database

Instant JChem is a desktop application for end user scientists. With Instant JChem you can create, explore and share chemical and non chemical data in local and remote databases without additional administration. Instant JChem has a wide and growing range of functionality including customizable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions and range of plotting and visualisation options.
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See also : A review of Instant JChem

Other tools from ChemAxon
Marvin
JChem

IQmol:- molecular editor and visualisation

IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

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IR Spec Check:- iPhone infrared spectral analysis

IR Spec Check is designed for organic chemists and students to quickly analyze absorbance peaks from an infrared spectroscopy graph. IR Spec Check recognizes over 75 absorbance frequencies and matches frequencies with possible R-groups. IR Spec Check's ranking system displays R-Groups based on how accurately your peak falls