The following sites are
related to software that may be of interest to
- Abbreviated Profile of Drugs (APOD) is a web-based decision and
prediction program for drug discovery - http://www.ApodVision.com
- 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.
The Amsterdam Density Functional
(ADF) package is software for first-principles electronic structure
calculations. ADF is used by academic and industrial researchers in such
diverse fields as pharmacochemistry and materials
science. It is particularly popular in the research areas of
homogeneous and heterogeneous catalysis, inorganic chemistry, heavy
element chemistry, various types of spectroscopy, and biochemistry.
- 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
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 - http://www.simulations-plus.com/
- Adun - Biomolecular Simulator. The environment for developing new
algorithms in molecular simulations (distributed under GPL Licence).
- Advanced Chemistry Development -- http://www.acdlabs.com/
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 http://biocomp.chem.uw.edu.pl/A3D 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 -- http://www.ahsystem.com/
- Agile Molecule -- Scientific Software for Chemists. Look at the catalog
- AMBER -- Molecular Dynamics Program -- http://ambermd.org/
- ALOGPS, CLOGP, KOWWIN ,XLOGP, IA_LOGP -- logP and logS calculator on
- AMSOL -- semiempirical quantum chemistry program (gas phase and
- 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
- 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
- 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
Hyde provides visual feedback at atomic detail.
- ReCore http://www.biosolveit.de/ReCore/
instantaneously generates scaffold replacement ideas with the objective,
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++ Library of Genetic Algorithm Components -- http://lancet.mit.edu/ga/
- CABS-dock - web server for protein-peptide docking. It is freely available
to all users at http://biocomp.chem.uw.edu.pl/CABSdock 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
http://biocomp.chem.uw.edu.pl/CABSflex 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
http://biocomp.chem.uw.edu.pl/CABSfold 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. http://www.chemcomp.com -- A leading provider of computational applications aimed at drug
- 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 -- 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. --
- 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 --
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
- DiscoveryGate - Online access to integrated primary literature, secondary
databases, and authoritative reference works
- DeMon DFT Package-- http://www.demon-software.com/public_html/index.html
- Dragon--able to calculate 5270 molecular descriptors, it has a nice
interface and runs on Windows and Linux PC's --
- 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 --
- 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 Firefly (formely PC 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 --
SWISS-PDB VIEWER: http://www.expasy.org/spdbv/
- HYPERCUBE. INC. -- http://www.hyper.com/
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.
- 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 --
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/
- 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/
- 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 http://www.univ-reims.fr/Labos/UPRESA6013/GNOSIE/LSD/
- 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 -- 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 --
- MOLCAS -- quantum chemistry software package http://molcas.org 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 -- 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
- 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
- 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\
- 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/
- Open Babel-- Program designed to interconvert a number of file formats used in molecular modeling -- http://openbabel.org/wiki/Main_Page
- 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/
- PlasmidBASE --
PlasmidBASE is a multi-platform
web interface software for storage and sharing of plasmid data. It
provides electronic plasmid data security and increases materials
reusability according to Good Scientific Practice Guidelines.
Built-in BLAST algorithm allows database searching DNA/protein queries.
Software is offered for unlimited number of users within research
- Polar -- electrochemical simulation and data analysis
- PREMIER Biosoft -- Software for molecular biologists.
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.
- ProBis -- Protein Binding Sites Detection:
Algorithm for detection of structurally similar protein binding sites
by local structural alignment.
- Prospect 2--PROSPECT is a threading-based protein structure prediction
- PyMOL-- Free and unrestricted open-source molecular graphics system -- http://pymol.sourceforge.net/
- Q-chem -- ab initio and DFT molecular modeling package
- Qmol -- An OpenGL based molecular viewer for Windows http://www.dnastar.com/products/qmol/index.html
- 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 -- 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/
- 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
- 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.
- 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 ( http://wavefun.com/products/spartan.html )
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
- 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://www.sunsetmolecular.com/ --
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 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
- Symbolic Algebra Package -- Maple -- http://www.maplesoft.com/
- Synergy Software -- Terminal Emulators -- http://www.synergy.com/
- 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
- TURBOMOLE -- Program Package for ab initio Electronic Structure
Calculations -- http://www.turbomole.com/
- UNIVIS-2000 -- Molecular Visualization Package from University of Pune.
Free for Academia.
- 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
is an integrated platform for Computer Aided Drug Design (CADD) and molecule
discovery available for both Windows® and Linux platforms.
suite provides complete toolkit to scientists to perform all scientific
functions required to pursue structure based as well as ligand based
- VMD Molecular Visualization
Software -- http://www.ks.uiuc.edu/Research/vmd/
- Wavefunction -- http://www.wavefun.com/
- WHATIF - sequence analysis package -- http://swift.cmbi.kun.nl/whatif/
- 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
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:
Email: jkl at ccl dot net.