Protein Structures

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  • Abbreviated Profile of Drugs (APOD) is a web-based decision and prediction program for drug discovery -
  • Accelrys- Molecular modeling, simulation, and informatics software for life and material sciences --
  • ACD/logP Freeware -- download to your desktop and predict logP values from structure.
  • ADF Modeling Suite -- developed and distributed by Software for Chemistry & Materials (SCM)
    Based around Amsterdam Density Functional, the ADF Modeling Suite has molecular & periodic DFT, semi-empirical, reactive MD, and fluid thermodynamic capabilities with an integrated GUI. It is used by researchers for many different applications in chemistry, materials science and chemical engineering.
  • ADME DB -- ADME DB is a database containing the latest and most comprehensive data on interactions of substances with Drug Metabolizing Enzymes and Drug Transporters. It is designed for use in drug research and development, including drug-drug interactions and ADME (Absorption, Distribution, Metabolism and Excretion) studies. The information is organized by category (therapeutic area), drug name, enzyme, reaction, and type. ADME DB is supported by chemical/metabolite structures as well as kinetic values found in the literature. The database is available online and completely searchable by keywords or chemical structures. Advanced searches are also available to support investigational studies on drug-drug interactions.
  • ADMEWORKS DDI Simulator -- ADMEWORKS DDI Simulator is a software application for assessing the risk of potential drug-drug interactions, allowing the user to perform both quantitative simulations of Competitive and Mechanism-based inhibitions.
  • ADMEWORKS ModelBuilder -- ADMEWORKS ModelBuilder is a tool dedicated for building QSAR/QSPR models that can later be used for predicting various chemical and biological properties of compounds. A set of data on molecular structures and their respective experimental values of the property of interest is a prerequisite for every model building. Two classes of models (Qualitative and Quantitative) can be built using various algorithms.
  • ADMEWORKS Predictor -- ADMEWORKS Predictor is a high-speed virtual (in silico) screening system intended for simultaneous evaluation of the ADMET properties of compounds. It complements existing In Silico technologies for evaluating pharmacological properties. Simultaneous evaluation of the pharmacological as well as the ADMET properties of compounds is useful in the discovery phase to produce balanced quality hits, and also in the lead optimization phase to lessen the occurrence of faulty leads.
  • ADMET Predictor - software for predicting and modeling the ADMET (Absorption, Distribution, Metabolism, Elimination, and Toxicity) of chemicals directly from molecular structure -
  • Adun - Biomolecular Simulator. The environment for developing new algorithms in molecular simulations (distributed under GPL Licence).
  • Advanced Chemistry Development -- Developers of chemical property prediction software and spectroscopic databases.
  • Aggrescan3D - web server for prediction of aggregation propensity in protein structures and rational design of protein solubility. It is freely available to all users at and there is no login requirement. In dynamic mode, A3D takes into account the flexibility of natural and designed proteins.
  • AHSystems Group -- Chemistry and Physics software reseller --
  • Agile Molecule -- Scientific Software for Chemists. Look at the catalog at:
  • AMBER -- Molecular Dynamics Program --
  • ALOGPS, CLOGP, KOWWIN ,XLOGP, IA_LOGP -- logP and logS calculator on the Internet--
  • AMSOL -- semiempirical quantum chemistry program (gas phase and solvation).
  • APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems --
  • ArgusLab 3.0 -- Molecular Modeling Software --
  • Automatic Format conversion of Molecular Structure Files by Corina --


  • Basis Set library for ab initio programs --
  • BioSolveIT -- Software solutions for structure and ligand-based molecular design --
    • 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 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 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 --



  • C++ Library of Genetic Algorithm Components --
  • CABS-dock - web server for protein-peptide docking. It is freely available to all users at and there is no login requirement. CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone in the default mode. In the advanced mode, CABS-dock also enables large-scale flexibility of protein receptor structure. CABS-dock animation movies are available at
  • CABS-flex - web server for fast simulations of protein structure fluctuations. It is freely available to all users at and there is no login requirement. CABS-flex was shown to be an efficient alternative to classical all-atom molecular dynamics. Also, it has been shown, that relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. CABS-flex animation movies are available at
  • CABS-fold - web server for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). It is freely available to all users at and there is no login requirement. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process.
  • CambridgeSoft Software -- CambridgeSoft Corporation is a leading supplier of discovery, collaboration, and knowledge enterprise solutions, desktop software, scientific databases and consulting services to the pharmaceutical, biotechnology, and chemical industries. The Company provides enterprise solutions, desktop software, scientific databases, and professional services for biotechnology, drug discovery and chemical research, including software, databases, and web sites which enable customers to create, analyze and communicate chemical, biological, and scientific information more effectively.
  • Cell Illustrator -- Cell Illustrator is a powerful tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory networks as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.
  • Chemical Computing Group Inc. -- A leading provider of computational applications aimed at drug discovery
    MOE – MOE (Molecular Operating Environment) is an integrated drug discovery software platform --
  • Chemical Markup Language --
  • 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 --
  • Chemistry Software and Information Resources (CSIR) --
  • ChemTK -- a cheminformatics toolkit for Windows --
  • 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. --
  • CLIFF -- is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: --
  • CMDBioscience, LLC -- CMD bioscience ( ) 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 --
  • Computational Chemistry -- Providing excellent software for research and higher education.
  • Computational Science and Engineering Online -- ( ) - 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.deCOSMOtherm (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.
  • Cresset -- ligand-based and structure-based solutions for drug discovery -- ( Software: Intuitive tools for outstanding design
  • Culgi BV -- 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.



  • 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 --






  • ImageWave EHS Enterprise Software Solution - 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 -- Runs on OS X, Windows and Linux.
  • JOELib -- An open source computational chemistry package written in Java
  • Jmol -- A free open source molecule viewer


  • 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 --
  • Leadscope, Inc. -- chemoinformatics software and databases: FDA Toxicity Database, FDA SAR Genetox Database, Predictive Data Miner and more (see the Website: for a full list of products and services).
  • Linux Scientific Software --
  • LiqCryst -- LiqCryst is a MS-Windows-based application that allows easy access to a unique database of structures and properties of liquid crystalline compounds. The LiqCryst database contains information about currently known thermotropic liquid crystalline compounds. LiqCryst covers all aspects of liquid crystal research: material properties, display technology, theory, basic research and applications.
  • LSD program -- Logic for Structure Determination, searches the molecular structures that are compatible with NMR spectroscopic data


  • 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.
  • Materials Design, Inc. -- Molecular modeling and simulation environment with builders and job management tools for inorganic materials --
  • MDL QSAR - Comprehensive QSAR modeling system --
  • MicroSimulations --
  • MIPSIM: is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials --
  • Mol2Mol: molecule file conversion,manipulation and utility program --
  • MOLCAS -- quantum chemistry software package or
  • 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 --
  • MolSoft -- 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--\





  • 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.
  • Schrodinger, Inc.'s -- Computational Chemistry Software --
  • Scienomics -- Software for Materials R & D, modeling and simulation.
  • Scientific Software Catalogue --
  • SCIGRESS -- SCIGRESS is a unique desktop molecular modeling software package that can apply a wide range of computational models to all types of molecular systems, from small organic molecules, to inorganics, polymers, materials systems and whole proteins. SCIGRESS speeds time-to-discovery by providing powerful computing and analytical tools designed for experimental scientists.
  • Seascape -- computational science company offering software, research consulting and software services --
  • Simulated Annealing or Adaptive Simulated Annealing, by Lester Ingber --
  • Simulated Biomolecular Systems Inc. (SimBioSys (TM)) Products for the pharmaceutical industry.
  • SKIN-CAD -- SKIN-CAD is a general simulation software for the skin and body pharmacokinetics following transdermal and topical drug delivery. SKIN-CAD predicts dynamic profiles of skin permeation and distribution and blood concentration under various modes of transdermal delivery. SKIN-CAD also analyzes the effects of metabolism and binding in the skin, dermal blood uptake, iontophoresis, and so on.
  • Spartan ( ) is a molecular modeling and computational chemistry application from Wavefunction, Inc. It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models and post-Hartree-Fock models.
  • SQS--is the Simple Queueing System that allows jobs to be run in sequence on a single machine --
  • Sunset Molecular Discovery, LLC -- -- WOMBAT-PK and WOMBAT: Pharmacokinetics and BioActivity Databases.
  • 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
  • Swiss PDF viewer--an application that provides a user friendly interface allowing to analyze several proteins at the same time --
  • Symbolic Algebra Package -- Maple --
  • Synergy Software -- Terminal Emulators --




  • VEGA1.4.3--program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). --
  • VLifeMDS ( ) (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 --



  • ZMM Software, Inc. -- -- 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).

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