Software-Related Sites

The following sites are related to software that may be of interest to computational chemists:

• Accelrys- Molecular modeling, simulation, and informatics software for life and material sciences -- http://www.accelrys.com/
   
  
• ACD/logP Freeware http://www.acdlabs.com/freelogp -- download to your desktop and predict logP values from structure.
   
  
• ADF, the Amsterdam Density Functional package ( http://www.scm.com/ ) for molecules and periodic systems.
   
  
• Adun - Biomolecular Simulator. The environment for developing new algorithms in molecular simulations (distributed under GPL Licence). http://diana.imim.es/Adun
   
  
• Advanced Chemistry Development -- http://www.acdlabs.com/ Developers of chemical property prediction software and spectroscopic databases

 

• AHSystems Group -- Chemistry and Physics software reseller -- http://www.ahsystem.com/
   
  
• Agile Molecule -- Scientific Software for Chemists. Look at the catalog at: http://www.agilemolecule.com/Software.html
   
  
• AMBER -- Molecular Dynamics Program -- http://amber.scripps.edu/
   
  
• ALOGPS, CLOGP, KOWWIN ,XLOGP, IA_LOGP -- logP and logS calculator on the Internet--http://www.vcclab.org/lab/alogps
   
  
• AMSOL -- semiempirical quantum chemistry program (gas phase and solvation). http://amsol.chem.umn.edu and http://www.makolab.com/amsol.
   
  
• APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems -- http://apbs.sourceforge.net/
   
  
• ArgusLab 3.0 -- Molecular Modeling Software -- http://www.planaria-software.com
   
  
• Artificial Life software -- http://alife.santafe.edu/alife/software/
   
  
• Automatic Format conversion of Molecular Structure Files by Corina -- http://www.molecular-networks.com/online_demos/corina_demo.html
   
  

• Babel, CLOGP, KOWWIN,XLOGP, IA_LOGP http://www.vcclab.org/lab/babel
   
  
• Babel-- Program designed to interconvert a number of file formats used in molecular modeling -- http://www.eyesopen.com/docs/html/babel/
   
  
• Basis Set library for ab initio programs -- http://www.emsl.pnl.gov:2080/forms/basisform.html
   
  
• BioSolveIT -- Software solutions for structure and ligand-based molecular design -- http://www.biosolveit.de
   
  
• Bio Online -- Biopharm Industry Info and Online Store for Life Sci Software -- http://www.bio.com/
   
  

 

• C++ Library of Genetic Algorithm Components -- http://lancet.mit.edu/ga/
   
  
• Chemical Computing Group Inc. http://www.chemcomp.com -- A leading provider of computational applications aimed at drug discovery
   
  
• Chemical Markup Language --
  http://cml.sourceforge.net
   
  
• Chemistry Software and Information Resources (CSIR) -- http://www.csir.org/index.html
   
  
• ChemTK -- a cheminformatics toolkit for Windows -- http://www.atomseek.com/Chemistry/Software/Cheminformatics/ChemTK_L96475/
   
  
• Chimera -- package for molecular modeling: atom-type identification, association of structures with sequence alignments, and interactive contouring of volume data (for example, electron density or electrostatic potential). Results from several molecular dynamics programs and from DOCK can be viewed and analyzed. Free for academia. -- http://www.cgl.ucsf.edu/chimera/
   
  
• CLIFF -- is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: -- http://www.mol-net.de/
   
  
• CMDBioscience, LLC -- CMD bioscience ( http://www.cmdbioscience.com/ ) specializes in the use of novel proprietary computational methods to model and engineer clinically important protein-protein and protein-peptide interactions. Our Affinity algorithm is designed to predict protein-protein / protein-peptide binding affinities; it is fast enough for use as a scoring function and will be made freely available to the academic community. Other key, proprietary computational tools employed by scientists at CMD Bioscience include Ensemble and Transcend. These groundbreaking search algorithms, when interfaced with Affinity, allow CMD scientists to efficiently design novel peptides and proteins
   
  
• CompuChem -- http://www.compuchem.com/
   
  
• Computational Chemistry -- http://www.computational-chemistry.co.uk/ Providing excellent software for research and higher education.
   
  
• Computational Science and Engineering Online -- ( http://cse-online.net ) - An innovative web-based Grid-enabled environment for molecular modeling and simulation
   
  
• Culgi BV -- http://www.culgi.com/ is dedicated to provide the chemical and pharmaceutical industry with revolutionary modelling tools for the rational design of soft matter formulations. Our flagship product is the Chemistry Unified Language Interface modelling library.
   
  

• DiscoveryGate - Online access to integrated primary literature, secondary databases, and authoritative reference works http://www.discoverygate.com
   
  
• DeMon DFT Package-- http://www.demon-software.com/public_html/index.html
   
  
• Dragon--able to calculate 1481 molecular descriptors, it has a nice interface and runs on Windows PC's -- http://www.disat.unimib.it/chm/Dragon.htm
   
  
• DSMM: a Database of Simulated Molecular Motions-- http://projects.villa-bosch.de/mcm/database/dsmm
   
  

• Elsevier MDL - scientific content, informatics framework and workflow applications that accelerate successful life sciences R&D by improving the speed and quality of scientists' decision making -- http://www.mdl.com

 

• FlexX -- Fast Flexible Docking Software http://www.biosolveit.de/flexx
   
  
• Force Field Explorer -- http://dasher.wustl.edu/ffe/
   
  
• FORTRAN-90 Tutorial -- http://www.cs.utk.edu/~london/MPPopt/additional.html
   
  
http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/fortran.html
 

• GAMESS ab initio program, and information on http://www.msg.ameslab.gov/ -- http://www.msg.ameslab.gov/GAMESS/GAMESS.html
   
  
Mark Gordon's Research Group. There is also PC GAMES: http://phys069b-2.chem.msu.ru/gran/gamess/.
 

• Gaussian Inc. -- http://www.gaussian.com
   
  
• gOpenMol -- http://www.csc.fi/gopenmol/
   
  
• Grace5.1.5: A WYSIWYG 2D plotting tool for the X Window System and M*tif --- http://plasma-gate.weizmann.ac.il/Grace/
   
  
• Gromacs MD Software -- http://www.gromacs.org/
   
  
• Guide to Available Mathematical Software (GAMS) -- http://gams.nist.gov/
   
  

• H-bonds: packages that display H-bons and more --
  AUTODOCK: http://autodock.scripps.edu/
  MOLEKEL: http://www.cscs.ch/molekel/>
  SWISS-PDB VIEWER: http://www.expasy.org/spdbv/
   
  
• HYPERCUBE. INC. -- http://www.hyper.com/
  HyperChem package: Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods, as well as density functional theory. HyperChem is applicable to macromolecules as well as small molecules and is scriptable.
   
  

• JOELib -- An open source computational chemistry package written in Java http://joelib.sourceforge.net/
   
  
• Jmol -- A free open source molecule viewer http://jmol.sourceforge.net/
   
  
L
• Lammps--is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lenard-Jonesium -- http://lammps.sandia.gov/
   
  
• Leadscope, Inc. -- chemoinformatics software and databases: FDA Toxicity Database, FDA SAR Genetox Database, Predictive Data Miner and more (see the Website: http://www.leadscope.com for a full list of products and services).
   
  
• Linux Scientific Software -- http://www.redbrick.dcu.ie/~noel/linux4chemistry/
   
  
• LSD program -- Logic for Structure Determination, searches the molecular structures that are compatible with NMR spectroscopic data http://www.univ-reims.fr/Labos/UPRESA6013/GNOSIE/LSD/
   
  
M
• Marvin Applets and Marvin Beans 2.10.5, JChem and JKlustor 1.7.3
  • - Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects.
  • - JChem provides chemical database searching capabilities by integration into relational database engines supporting SQL.
  • - JKlustor is a software for diversity calculations and clustering, which can generate and apply 2D molecular fingerprints.
  http://www.chemaxon.com/marvin/jnlp/index.html
  http://www.chemaxon.com/marvin/doc/for-mac-users.html
  http://www.jchem.com/doc/user/
  http://www.jchem.com/changes.html
  http://www.jchem.com/doc/admin/JKlustor.html
  http://www.chemaxon.com/marvin/demos.html
  http://www.jchem.com/examples.html
   
  
• MDL QSAR - Comprehensive QSAR modeling system -- http://www.mdl.com/products/predictive/qsar/index.jsp
   
  
• MicroSimulations -- http://www.microsimulations.com/
   
  
• MIPSIM: is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials -- http://cbbl.imim.es:8080/cbbl/publications-new/decaceres00/?searchterm=mipsim
   
  
• Mol2Mol 5.4: molecule file conversion,manipulation and utility program -- http://web.interware.hu/frenzy/mol2mol/index.html
   
  
• Molexel-- an interactive molecular graphics program to visualize molecular and electronic structure data from a number of electronic structure program outputs (Gaussian, Gamess, ADF...) as well as from XYZ and PDB files -- http://www.cscs.ch/molekel/
   
  
• MOPAC: new features of MOPAC 2002 and LinMOPAC2.0--http://www.ccl.net/chemistry/links/software/index.shtml\
   
  
N
• NetLib -- Library of Numerical Public Domain Software -- http://www.netlib.org/
   
  
• NIST -- Guide to Available Mathematical Software -- http://gams.nist.gov/
   
  
• Numerical Recipes Home -- online version of "Numerical Recipes" -- http://www.nr.com/
   
  
O,P,Q
• ORTEP -- Plot program -- http://www.ornl.gov/ortep/ortep.html
   
  
• Orbitron -- A gallery of Orbitals on Internet -- http://www.shef.ac.uk/chemistry/orbitron/
   
  
• Packmol--Creates an initial point for molecular dynamics simulations by packing molecules with a specified minimum-atom distance--http://www.ime.unicamp.br/~martinez/packmol
   
  
• PGPLOT -- Graphics Subroutine Library -- http://astro.caltech.edu/~tjp/pgplot/
   
  
• Polar -- electrochemical simulation and data analysis (http://www.electrochem.net, http://www.DrHuang.com).
   
  
• PREMIER Biosoft -- Software for molecular biologists. http://www.premierbiosoft.com
  Real Time PCR Design, Primer and Probe Design, Cloning & Plasmid Maps, Cross Species, Species Identification, Allele Identification, SNP Detection, SNP Genotyping, DNA Methylation, FRET Probes, Microarray Software, Tissue Microarray Sofwtare, Glycan, Glycosylation, etc.
   
  
• Prospect 2--PROSPECT is a threading-based protein structure prediction system--http://compbio.ornl.gov/structure/prospect2/
   
  
• PyMOL-- Free and unrestricted open-source molecular graphics system -- http://pymol.sourceforge.net/
   
  
• Q-chem -- ab initio and DFT molecular modeling package http://www.chemistry-software.com/qchem/qchem.htm
   
  
• Qmol -- An OpenGL based molecular viewer for Windows http://www.dnastar.com/products/qmol/index.html
   
  
R
• RASMOL -- http://www.umass.edu/microbio/rasmol
   
  
S
• SageMD -- Visualizer/builder for crystal structures and interfaces. Classical MM/MD. Support for popular file formats for export/import. Extensve database of inorganic structures. Free for academia and inexpensive for industrial researchers. http://sagemd.com
   
  
• Schrodinger, Inc.'s -- Computational Chemistry Software -- http://www.schrodinger.com/
   
  
• Scienomics -- http://www.scienomics.com. Software for Materials R & D, modeling and simulation.
   
  
• Scientific Computing & Modelling -- http://www.scm.com
   
  
• Scientific Software Catalogue -- http://www.scitechint.com/
   
  
• Seascape -- computational science company offering software, research consulting and software services -- http://www.seascapelearning.com
   
  
• Simulated Annealing or Adaptive Simulated Annealing, by Lester Ingber -- http://alumni.caltech.edu/~ingber/
   
  
• Simulated Biomolecular Systems Inc. (SimBioSys (TM)) http://www.simbiosys.ca Products for the pharmaceutical industry.
   
  
• SQS--is the Simple Queueing System that allows jobs to be run in sequence on a single machine -- https://sourceforge.net/projects/sqs/
   
  
• Sunset Molecular Discovery, LLC -- http://sunsetmolecular.com/ -- WOMBAT-PK and WOMBAT: Pharmacokinetics and BioActivity Databases;
  ChemGPS: Chemical Global Positioning System
   
  
• SWizard is a user-friendly program (OS: MS Windows NT/2000/XP) for postprocessing spectral data. A spectrum is calculated as a sum of Gaussian or/and Lorentzian bands or the mixture of these functions please check http://www.sg-chem.net/swizard/
   
  
• Swiss PDF viewer--an application that provides a user friendly interface allowing to analyze several proteins at the same time -- http://www.expasy.org/spdbv/
   
  
• Symbolic Algebra Package -- Maple -- http://www.maplesoft.com/
   
  
• Synergy Software -- Terminal Emulators -- http://www.synergy.com/
   
  
T
• TINKER Molecular Modeling Software -- http://dasher.wustl.edu/tinker/
   
  
• Transient V2.52 -- A new reaction-diffusion equations solver -- http://transient.mkolar.org
   
  
• Tripos, Inc. -- software products and services for compound research in pharmaceutical, -- http://www.tripos.com biotechnological, and related organizations worldwide
   
  
U
• UNIVIS-2000 -- Molecular Visualization Package from University of Pune. Free for Academia. http://chem.unipune.ernet.in/univis.html
   
  
V
• VEGA1.4.3--program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). -- http://www.ddl.unimi.it/
   
  
• VMD Molecular Visualization Software -- http://www.ks.uiuc.edu/Research/vmd/
   
  
W
• Wavefunction -- http://www.wavefun.com/
   
  
• WHATIF - sequence analysis package -- http://swift.cmbi.kun.nl/whatif/
   
  
X,Y,Z
• ZMM Software, Inc. -- http://www.zmmsoft.com -- Molecular Modeling and Simulation Software (MVM viewer is a freeware, ZMM is a molecular modeling and simulation system that runs on Windows and Unix/Linux).
   
  

A large list of links to chemistry software makers is also available at http://www.liv.ac.uk/Chemistry/Links/softwarecomp.html -- Links for Chemists

Disclaimer: The list is provided as a service to the CCL community. However, no guarantees are given as to the suitability or accuracy of this list. The text and the links to web sites were often provided by vendors or taken from other web sites. Some of the information may already be obsolete, since the list is not aggresively maintained or reviewed. Please provide additions or correction to this list by contacting the CCL.NET manager:
Jan Labanowski.
Email: jkl at ccl dot net.