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Software-Related Sites

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

A| B| C| D| E| F| G| H| I| J| K| L| M| N| O| P| Q| R| S| T| U| V| W| X| Y| Z
 
A B
  • Babel, CLOGP, KOWWIN,XLOGP, IA_LOGP http://www.vcclab.org/lab/babel
     
  • Basis Set library for ab initio programs -- https://bse.pnl.gov/bse/portal
     
  • BioSolveIT -- Software solutions for structure and ligand-based molecular design -- http://www.biosolveit.de
    • PoseView http://www.biosolveit.de/PoseView/ is a software tools to generate 2D-images (png, svg and pdf) of 3D Protein-Ligand complexes. Note that PoseView images are available for the majority of PDB-structures on the PDB web site.
    • HYDE http://www.biosolveit.de/Hyde/ in an entirely new approach to assessing binding affinities. Hyde is entirely based on physics-principles and has not been trained or calibrated on experimental data. Hyde provides visual feedback at atomic detail.
    • ReCore http://www.biosolveit.de/ReCore/ instantaneously generates scaffold replacement ideas with the objective, to leave the 'old' side chains in place. It is also applicable in fragment-merging, fragment-linking and fragment-growing scenarios.

     
  • Bio Online -- Biopharm Industry Info and Online Store for Life Sci Software -- http://www.bio.com/
     

    •  
C
  • 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
     
  • Chemissian: quantum chemistry program for visualizing electron/spin density distribution and UV-VIS spectra, plotting molecular orbital energy level diagrams, calculating atomic orbital populations, contributions of atoms and fragments to MOs. Chemissian supports output files of US-GAMESS, PC-GAMESS/Firefly and Gaussian quantum chemistry software packages -- http://www.chemissian.com/.
     
  • 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
     
  • COSMOlogic -- Software for Life Sciences, Chemical Engineering and Quantum Chemistry. http://www.cosmologic.de: COSMOtherm (quantitative calculation of solvation mixture thermodynamics based on quantum chemistry), COSMOfrag (a tool that performs the rapid, automated fragmentwise construction of approximate sigma-profiles of larger molecules), COSMOsim (uses COSMO-RS method to assess crucial information for most ADME properties), COSMOmic (describes micelles or biomembranes) and distribution of other computational chemistry packages.
     
  • 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.
     
D E
  • 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

    •  
F G H I,J,K
  • ImageWave EHS Enterprise Software Solution - http://www.imagewave.com. This EHS solution provides MSDS Management (MSDSFinder), Environmental Reporting (including SARA 313 and Tier II), Container Labeling, MSDS Authoring, MSDS directory, MSDS Scanning/Updating Service and more.
     
  • IQmol open-source molecular editor and vizualization package -- http://www.iqmol.org/. Runs on OS X, Windows and Linux.
     
  • JOELib -- An open source computational chemistry package written in Java http://sourceforge.net/projects/joelib/
     
  • Jmol -- A free open source molecule viewer http://jmol.sourceforge.net/
     
L 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/
     
  • Materials Design, Inc. -- Molecular modeling and simulation environment with builders and job management tools for inorganic materials -- http://www.materialsdesign.com
     
  • 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: molecule file conversion,manipulation and utility program -- http://www.gunda.hu/mol2mol/index.html
     
  • MOLCAS -- quantum chemistry software package http://molcas.org or http://www.teokem.lu.se/molcas/.
     
  • 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/
     
  • MolSoft -- http://www.molsoft.com/: Molsoft is a La Jolla, California based company that is a primary source of new breakthrough technologies in: molecular graphics and visualization, molecular modeling, docking and virtual screening, computational biology and cheminformatics.
    • ICM-Browser Molecule Visualization
      • ICM-Browser (Free Download) -- Software for browsing molecules and making fully-interactive slides for embedding in PowerPoint and the Web using ActiveiCM.
      • ICM-Browser-Pro -- A high quality visualizer and annotator for three dimensional molecular structures, sequences and alignments, chemical spreadsheets and biological data.
      • ActiveICM (Free Download) -- Enables you to view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers such as Internet Explorer, Safari and Mozilla Firefox.
    • ICM-Pro and Modules Desktop Modeling
      • ICM-Pro -- Easy-to-use and complete desktop-modeling environment for a biologist or a chemist interested in molecular structure and function.
      • ICM-Homology - Modeling -- High-throuput molecular modeling, loop modeling and refinement program.
      • ICM-VLS - Virtual Ligand Screening -- A structure-based drug design program allows you to dock and score millions of compounds. An efficient and proven approach for lead discovery.
    • ICM-Chemist: Cheminformatics Tools
      • ICM-Chemist -- A standalone suite of programs for chemical drawing and editing, chemical database generation, chemical searching, clustering, and enumeration.
      • ICM-Chemist-Pro -- A standalone cheminformatics products containing a wide set of 3D chemical tools, chemical superposition, 3D interactive ligand-receptor editing, and QSAR.
    • Chemical Management Tools
      • MolCart -- MolCart allows you to store large chemical compound libraries for searching and analysis. Moreover, it uses a fast relational database which is freely available without any limitations.
      • MolCart Compounds -- MolCart Compound Database is an up-to-date collection of vendor compound databases.

    •  
  • MOPAC: new features of MOPAC 2002 and LinMOPAC2.0--http://www.ccl.net/chemistry/links/software/index.shtml\
     
N O,P,Q R S T U 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/
     
  • VLifeMDS (www.vlifesciences.com ) (VLife Molecule Design Suite) is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows® and Linux platforms. This integrated suite provides complete toolkit to scientists to perform all scientific functions required to pursue structure based as well as ligand based discovery approaches.
     
  • VMD Molecular Visualization Software -- http://www.ks.uiuc.edu/Research/vmd/
     
W 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.

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