Molecular Modeling Software

Molecular Mechanics

• AMBER Molecular simulation programs
• CHARMM
• Molecular Monte Carlo at Cooper Union Department of Chemistry
• PNL MSCF Software Suite
• VMD  - Visual Molecular Dynamics
• MOLDY  - Free MD program
• GROMACS Molecular Dynamics on Parallel Computers
• GROMOS Dynamic Modelling of Molecular Systems
• MacroModel - Molecular Modelling
• MSI/Biosym Molecular Modelling Software
• NAMD - Scalable Molecular Dynamics
• PMD - Parallel Molecular Dynamics which is also archived at CCL
• SimChemistry molecular dynamics simulation for chemistry teaching
• TINKER package for molecular mechanics and dynamics
• TransCube, TransFreq, Molnf and Scian Programs for visualising Gaussian 94 output and Scientific Visualisation
• SYBYL - software from Tripos
• TURBOLMOL - Ab initio electronic structure calculations -mainly on the SCF level of theory  
• X-PLOR- MM program free for Academics
• DNAtools-Web tools to analyze DNA - Gabrielyan!

Quantum Chemistry

• GAMESS
• NWCHEM High-perfomancs massively parallel QC program  and more
  now combined with MPQC , PETSC - CCA activity
• PSI3 - Crawford, Valeev, Sherill QC program and Integral package
• LibintGaussian Integral library of Valeev in C
• Open BabelInterface between Scientific Programs
• MOLCAS Quantum chemistry software at Lund University
• MPQC Home Massively Parallel QChem program (C++) in Sandia
• MOLPRO an ab initio package by H.-J. Werner and P. J. Knowles
• GAMESS-UK
• Gaussian
• HyperCube Inc.
• Dalton
• ACES II Advanced Concepts in Electronic Structure
• ADF (SCM company site) Amsterdam Density Functional program
• ATMOL an ab initio program
• CADPAC -- The Cambridge Analytic Derivatives Package
• COLUMBUS general ab initio electronic structure calculations
• CRYSTAL - ab initio electronic structure calculations on periodic systems.
• COSMO-RS computational chemistry software for problems of solvation and the liquid phase
• DeFT - A gaussian density functional program
• Huckel Calculator for WIndows 95 & NT
• MolEdit an editor for quantum chemistry input files
• PSI 2.0 - Wavefunction Evaluator
• Python source code for computational chemistry
• Q-Chem, the Program
• Quantum Chemistry Program Packages
• Schrödinger Inc. - Electronic structure software
• Wavefunction Inc. - makers of Spartan, etc. 
• ICON-EDiT - Extended Huckel Molecular Orbital and Oscillator Strength Calculation Package
• UK CCWPUK  Computational Chemistry Working Party

Intermolecular Interactions and Docking

• AutoDock
• DOCK "docking" molecules
• FlexX automatic prediction of receptor-ligand interactions
• HYDRO calculation of hydrodynamic properties
• LIGPLOT Program for automatically plotting protein-ligand interactions
• SPROUT de novo ligand design 
• STALK: A Molecular Docking System
• Viseur visualize G Protein-Coupled Receptors
• Ilya Vakser Lab, GRAMM package

Solid State and Surfaces simulations

• Gulp Simulation on 3D periodic solids, gas phase clusters and isolated defects

Bioinformatics

• Bioinformatics Host site for many bioinformatics projects

Electron Scattering

• MOLSCAT - Quantum non-reactive molecular scattering program

Electrostatics calculations

• GRASP Graphical Representation and Analysis of Structural Properties
• PEP Protein Electrostatics.
• SOLPRO prediction of Solution Properties of rigid macromolecules and bioparticles
• Poisson-Boltzmann stuff
• KARLSBERGprogram for Monte-Carlo titration of proteins
• Bashford Group Homepage

Benchmark for computational chemistry applications

• CFS benchmarks

Molecular visualization and editing

• B(Biomer) of J.White  a Java-based, on-line biomolecular modeling package
• CambridgeSoft Corporation (ChemDraw etc)
• ChemSketch from ACD
• ChemWeb from SoftShell Online: a tool for creating chemical structure images for HTML documents
• Cn3D See in Three-Dee for the Macintosh
• CrystalMaker Real-time crystallography for personal computers
• dejavu - Python and OPENGL based visualization program
• EyeChem - Explorer modules for molecular modelling  
• Fungimol An extensible system for designing atomic-scale objects 
• GAP (Geometric analysis programs) 
• Garlic free molecular visualization program
• Ghemical Homepage free package for molecular visualization and modeling
• gOpenMol - Graphics Interface to the OpenMol programs
• HDBPLUS Hydrogen Bond Calculation Program
• The HOLE suiteHOLE was written to allow the visualization and analysis of the holes through atomic models of ion channels
• HyperCube - HyperChem, ChemPlus and HyperNMR
• Molsoft L.L.C. HomeICM and ICM-lite(free) programs
• Jmol An open Source molecule viewer and editor 
• JSV Java Structure Viewer 
• LIGPLOT Program for automatically plotting protein-ligand interactions  
• MacroModel - Molecular Modelling
• MDL Products - including Chime, ISIS/Draw and ISIS/Base
• MOLDEN visualization of molecular and electronic structure
• MOLDRAW Molecules and crystals on a personal computer
• MOLMOL a molecular graphics program
• MolGen - Molecular modelling for PCs  
• Molecule for Macintosh which can also run on a PC using ARDI's Executor
• The Molecular Modelling Toolkit
• MolPOV a graphics file converter for POVRAY
• MoluCAD molecular modeling and visualization tool
• Molscript - molecular graphics as Postscript files
• MolView and Molview Lite - Molecular rendering for the Macintosh 
• Moviemol - the molecular animation program 
• OpenMol OpenMol Community
• Oxford Molecular computer-aided chemistry and bioinformatics software
• PovChem Chemical Imaging using Persistence of Vision ray (POV-RAY) tracing
• PyMOL Home Page - Completely free PYTHON integrated Molecular graphics program
• Rasmol - Molecular visualisation program:
• Rasmol derived: Programs for Unix, VMS, Macintosh and Windows
• RasMol Documentation
• Chime Rasmol based plug-in for Netscape
• RasMol FAQ sheet
• Raster3D - 3D molecular graphics generator
• Re_View - Dynamic reaction data visualization and analysis tool
• REDUCE: Build Hydrogens on your Model
• Ribbons Ribbon Diagrams to show protein structure
• SCULPT; molecular modeling system
• Swiss-Pdb Viewer
• ScientificGL - www.CompBio.net
• SYBYL - software from Tripos
• Viseur visualize G Protein-Coupled Receptors 
• UNICHEM molecular modeling package
• VIEWMOL graphical front end for some quantum chemical and molecular modelling programmes
• XMol - An X Windows-based molecule rendering and animation package and the XMol FAQ

Molecular Surface Computations

• Molecular Surface Package of Connolly$500 compute cavities and more
• MSMS Molecular Surface Computation program

Protein Structure Prediction and analysis 

• WHATIFversatile protein structure analysis program
• PredictProtein
• PSIPRED Protein Structure prediction server
• Prometheus Software for Molecular Design  

Chemioinformatics 

• Frowns Chemioinformatics system
• PyDaylight at MUG2000
• DaylightChemical Information company/software

Parallelization, IO and distributed programming in computational chemistry

• CACTVS A Chemistry Algorithm Development Environment

Molecular format converters and other utilites

• Babel Molecular Format conversion program, assignment of hybridization and more
• CAMO Software: specialises in multivariate data analysis software, in particular Unscrambler
• Mol2Mol - chemical file converter and geometry utilities
• pyBabel overview- Python reimplementaion of some BABEL functionality
• NAB molecular manipulation language

Other lists of computational software

• InfoChem.UK
• Linux for Chemistry$35 CD ROM with free linux chemical/biological programs
• Linux4Chemistry - Linux software for chemistry
• Chemistry Software on Links to Go site
• Scientific Applications for Linux
• WWW Computational Chemistry Resources from swin.edu au 
• Chemistry, biochemistry and biotechnology software for Silicon Graphics computers
• Chemistry software for MS-DOS
• Chemistry software for MS-Windows
• CCL.NET Chemistry software list
• The NIH software index
• Software Reviews from the CTI Centre for Chemistry
• Yale Molecular Biophysics Biochemistry Center Structural Biology