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Chemoinformatics Software

This is only a very incomplete selection of chemoinformatics tools. However, it shows the variety of tools. We include this page to illustrate how demanding it is to select the right tool for the right job. We don't know all of them, but we can help you. Please feel free to ask us. Other links, that give an overview:

DSSTox

 

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3E Company Inc. (MSDS software) US
A
Accelrys- Molecular modeling, simulation, and informatics software for life and material sciences -- http://www.accelrys.com/
ACD/Labs - Advanced Chemistry Development Inc. CA
Acorn NMR US
ACS PUBLICATIONS, CAS AND STN
Adept Scientific UK
Adun - Biomolecular Simulator. The environment for developing new algorithms in molecular simulations (distributed under GPL Licence). http://diana.imim.es/Adun
Advanced Algorithms for Parallel Molecular Dynamics: The program PMD -- http://tincan.bioc.columbia.edu/Lab/pmd/
Advanced American Biotechnology US
ADVANCED CHEMISTRY DEVELOPMENT (ACD/LABS)
Agranova UK
AHSystems Group -- Chemistry and Physics software reseller -- http://www.ahsystem.com/
AKTS CH
Albany Molecular Research Inc. US
AlChemie Software NL
ALOGPS, CLOGP, KOWWIN ,XLOGP, IA_LOGP -- logP and logS calculator on the Internet--http://www.vcclab.org/lab/alogps
AM Technologies US
AMBER -- Molecular Dynamics Program -- http://www.amber.ucsf.edu/amber/amber.html
AMSOL -- semiempirical quantum chemistry program (gas phase and solvation). http://amsol.chem.umn.edu and http://www.makolab.com/amsol.
Amsterdam Density Functional (ADF) NL
APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems -- http://agave.wustl.edu/apbs/
Arbeitskreis Computer im Chemieunterricht (AK) DE
ARGENTA DISCOVERY
ArgusLab 3.0 -- Molecular Modeling Software -- http://www.planaria-software.com
Artificial Life software -- http://alife.santafe.edu/alife/software/
Aston Scientific Ltd. UK
AUREUS PHARMA
AUTODOCK: http://www.scripps.edu/pub/olson-web/dock/autodock/
Automatic Format conversion of Molecular Structure Files by Corina -- http://www2.ccc.uni-erlangen.de
B
Babel-- Program designed to interconvert a number of file formats used in molecular modeling -- http://www.eyesopen.com/babel.html
Babel, CLOGP, KOWWIN,XLOGP, IA_LOGP http://www.vcclab.org/lab/babel
Backbone-dependent rotamer library by Roland Dunbrack -- predicting sidechain conformations --Http://www.fccc.edu/research/labs/dunbrack/index.html
Basis Set library for ab initio programs -- http://www.emsl.pnl.gov:2080/forms/basisform.html
Bio Online -- Biopharm Industry Info and Online Store for Life Sci Software -- http://www.bio.com/
BioByte Corp. US
BIOMED CENTRAL
BIO-RAD LABORATORIES, INFORMATICS DIVISION
BioRad Sadtler US
Bioreason US
BioSolveIT -- Software solutions for structure and ligand-based molecular design -- http://www.biosolveit.de
BIOSYM Software manuals on line -- http://www-bio.unizh.ch/home.html
BIOTAGE
BIOWISDOM
Bitwixt Software Systems LLC US
C
C++ Library of Genetic Algorithm Components -- http://lancet.mit.edu/ga/
Cambridge Analytical Derivatives Packages (CADPAC) -- http://www.ch.cam.ac.uk/CUCL/theo/theo.html
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC) 
Cambridge Scientific Abstracts US
Cambridge Software UK
CAMBRIDGESOFT CORPORATION
Camo ASA (Multivariate Analysis) NO
Catalog of Molecular Graphics Packages -- http://www.catalytica-inc.com/camd/
CEREP
CHAM (Fluid dynamics) UK
Character tables for chemically important point groups -- http://www-theory.mpip-mainz.mpg.de/~gelessus/group.html
CHARMm Manuals on line -- http://www.ki.si/charmm/charmm.html
Chem Sources (Database Co.) US
Chem1Ware Ltd. CA
Chem2Pac BR
ChemAxon HU
CHEMBRIDGE
ChemBuddy PL
ChemDBsoft US
Chemdex Co. (Chemical database / sales) US
CHEMDIV
Chemical Computing Group Inc. CA
Chemical Computing Group Inc. http://www.chemcomp.com -- A leading provider of computational applications aimed at drug discovery
Chemical Concepts (Wiley-VCH subsidiary) DE
Chemical Kinetics Simulator (CKS)
Chemical Markup Language -- http://www.xml-cml.org/ http://cml.sourceforge.net
ChemInform Saint-Petersburg (CISP) Ltd. RU
ChemInnovation Software Inc. US
CHEMISTRY CENTRAL
Chemistry Software and Information Resources (CSIR) -- http://www.csir.org/index.html
Chemistry Software and Information Resources (CSIR) US
Chemistry Software 'dot' Com UK
CHEMIX (Scandinavian Chemistry Software) NO
Chemkey Search @ Heterodata Inc. / Emory US
CHEMNAVIGATOR
ChemNavigator Inc. US
Chemos Software UK
ChemPen 3D Molecular Structure Builder US
Chemsoft Ltd. UK
ChemSW Inc. US
ChemSymphony US
ChemTK -- a cheminformatics toolkit for Windows -- http://www.chemtk.com
Chemware (Educational) NZ
Chemware (LIMS) US
Cherwell Scientific UK
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/
Chrom Perfect (Justice Laboratory Software) US
CIDRUX PHARMINFORMATICS
CleoSci US
CLIFF -- is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: -- http://www.mol-net.de/
Cognitive Solutions Ltd. UK
CoHort Software US
COLLABORATIVE DRUG DISCOVERY
CompuChem -- http://www.compuchem.com/
CompuChem DE
COMPUDRUG
CompuDrug US
Computational Science and Engineering Online -- ( http://cse-online.net ) - An innovative web-based Grid-enabled environment for molecular modeling and simulation
Computer Animation Adds new dimensions to chemistry fundamentals -- http://bond.caltech.edu/index.html
CROSSREF
Crystal Impact DE
Crystal Structure Design AS NO
CrystalSoft Corp. AU
CTI for Chemistry @ Liverpool UK
Cubic Science US
CWM Global Search
CYPROTEX
D
DALI: Comparison of protein structures in 3D -- http://www.sander.embl-heidelberg.de/
DataApex Ltd. (Chromatography software) CZ
DataWeld Inc. (Chemical asset tracking) US
DAYLIGHT CHEMICAL INFORMATION SYSTEMS
DeMon2002 Binary demo for DFT and more -- http://www.deMon-software.com/public_html/demo.html
DeskTop Laboratories Inc. US
DialogChem UK
DIGITAL CHEMISTRY
Digital Chemistry Company UK
DiscoveryGate - Online access to integrated primary literature, secondary databases, and authoritative reference works http://www.discoverygate.com
Donley Technology (MSDS/Publishing) US
DOTMATICSL
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
Dundee Scientific UK
Dyadem International Ltd. (HAZOP, PHA, FMEA and RMP) CA
E
EduSoft LC US
EIDOGEN-SERTANTY
ELSEVIER
ELSEVIER MDL
Symyx (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
Environmental Data Services Ltd. (ENDS) UK
Equbits LLC. US
Erithacus Software Ltd. UK
Expertsoft GmbH CH
F
Falcon Software US
FDM Fiveash Data Management Inc. (Spectral Databases) US
FIZ CHEMIE BERLIN
FIZ KARLSRUHE
FIZ Karlsruhe (Database Access) DE
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 ttp://www.colorado.edu/ITS/docs/scientific/fortran/f90/tutorial/
French Creek Software US
FUJITSU
G
G&P Engineering Software US
G_covar in gromacs suite(version 3.0): Calculates and diagonalizes the (mass-weighted) covariance matrix -- http://www.gromacs.org/documentation/reference_3.0/online/g_covar.html
Galactic Industries (Instrument software) US
GALAPAGOS
GAMESS ab initio program, and information on http://www.msg.ameslab.gov/ -- http://www.msg.ameslab.gov/GAMESS/GAMESS.html
GAMESS Users List -- http://mineral.umd.edu/gamess-users/
Gaussian Inc. -- http://www.gaussian.com
Genetics Computer Group (Now part of Accelrys Inc.) US
gNMR for NMR simulation -- http://www.cherwell.com/ProdHome/gnmrhome.html
gOpenMol -- http://laaksonen.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/
GraphPad Software Inc. US
GRID, Re_View programs cor Molecular Modeling -- http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm
Guide to Available Mathematical Software (GAMS) -- http://gams.nist.gov/
GUM Workbench DK
Gussian Inc. US
H
Hampden Data Services Ltd. UK
H-bonds: packages that display H-bons and more  
hostDesigner @ PNL US
HSC Chemistry @ Outokumpu Research FI
Hypercube Inc. CA
I
ICD GmbH (LIMS) DE
ID Business Solutions (Chemical Data management software) UK
IDBS
ImageWave Corp. US
INFOCHEM
InfoCoatings SA CH
Infometrix US
INFORSENSE
Ingensis Ltd. UK
INPHARMATICA
Interprobe Chemical Services UK
INTUTE
IO INFORMATICS
ItemTracker UK
J
Java -- New Web browser which can even support http://java.sun.com/applets/applets/ChemicalModels/index.html Chemistry once installed. -- http://java.sun.com/
JCAMP-DX file reader (Dept. Chemistry UWI, Jamaica -- http://wwwchem.uwimona.edu.jm:1104/index.html
Jmol -- A free open source molecule viewer http://jmol.sourceforge.net/
JOELib -- An open source computational chemistry package written in Java http://joelib.sourceforge.net/
JOHN WILEY & SONS
K
Khem Products Inc. US
Kidger Optics UK
Kimberlyte Inc. US
Kinetic Technologies RU
KNOVEL CORPORATION
Kombyonyx.com UK
L
LabControl GmbH DE
LabSystems US
LABTECH US
LABTrack US
Labtronics Inc. US
LabWare (LIMS) US
LabWorldSoft DE
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://www.cs.sandia.gov/~sjplimp/lammps.html
L-Chem US
LCI Publisher DE
LEADSCOPE
Lexi-Comp Inc. US
LEXIS-NEXIS (Information service) US
LHASA LIMITED
Limathon Ltd. (Analytical Database Systems) UK
Linux Chemistry Software -- http://chpc06.ch.unito.it/chem_linux.html
Linux Scientific Software -- http://www.redbrick.dcu.ie/~noel/linux4chemistry/
LSD program -- searches the molecular structures hat are compatible with NMR spectroscopic data. http://www.univ-reims.fr/Labos/UPRESA6013/GNOSIE/LSD/
M
m2 Solutions LLC US
MacroModel mailing list -- http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html
Mark Gordon's Research Group. There is also PC GAMES: http://phys069b-2.chem.msu.ru/gran/gamess/.
Marvin
MathCad US
Mathtrek Systems US
MCH Multimedia CA
McIntosh Analytical Systems US
MDL Information Systems US (MDL is obsolete; it is now Accelrys)
MDL QSAR - Comprehensive QSAR modeling system -- http://www.mdl.com/products/predictive/qsar/index.jsp
MDL Sculpt -- 3D structural visualization and analysis http://www.mdl.com/products/predictive/sculpt/index.jsp
MicroSimulations -- http://www.microsimulations.com/
MicroSimulations US
MINER3D
MIPSIM: is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials -- http://www1.imim.es/modeling/mipsim/index.html/
Model Science Software Inc. US
Mol2Mol 5.4: molecule file conversion,manipulation and utility program -- http://web.interware.hu/frenzy/mol2mol/index.html
Molcas SE
MOLDEN: http://www.caos.kun.nl/~schaft/molden/CopyRight.html
Molecular Applications Group US
Molecular Discovery Ltd. UK/IT
Molecular Informatics Inc. (MII) US
MOLECULAR NETWORKS
Molecular Networks GmbH DE
Molecular Structure Corporation US
MOLEGRO
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/
Molfunction JP
MOLINSPIRATION
Molinspiration SK
Molpro documentation -- http://tcibm2.bham.ac.uk/molpro/molpro.html
MOPAC: new features of MOPAC 2002 and LinMOPAC2.0-- http://www.fqspl.com.pl/linmopac/default.html/\
MultiD Analyses AB SE
MultiSimplex AB (Experimental optimisation) SE
N
Naccess v2.0 - Atomic solvent accessible areas -- http://www.biochem.ucl.ac.uk/~roman/naccess/naccess.html
Negev Software Industries (Rotem Industries subsidiary) IL
NetLib -- Library of Numerical Public Domain Software -- http://www.netlib.org/
NIST -- Guide to Available Mathematical Software -- http://gams.nist.gov/
NLREG (Nonlinear Statistical Regression) US
Numerical Recipes Home -- online version of "Numerical Recipes" -- http://www.nr.com/
NUTS (NMR processing software)
O
OLI Systems US
OPEN EYE SCIENTIFIC SOFTWARE
Optive Research, Inc. -- software products and services for molecular modeling, simulation and research in pharmaceutical industry -- http://www.optive.com
ORBITAL VIEWER for Windows 2000-NT-XP -- http://www.voxeltime.com/Download/
Orbitron -- A gallery of Orbitals on Internet -- http://www.shef.ac.uk/chemistry/orbitron/
OriginLab (Formerly MicroCal) US
ORTEP -- Plot program -- http://www.ornl.gov/ortep/ortep.html
OUTSELL
Oxford Molecular (Now part of Accelrys Inc.) UK
P
Packmol--Creates an initial point for molecular dynamics simulations by packing molecules with a specified minimum-atom distance--h
PDBLib documentation, a C++ macromolecular class library -- http://cuhhca.hhmi.columbia.edu/bourne.html
Pedro's Biomolecular Research Tool, Database relating Proteins Structures and Sequences PROCHECK program, its source for the ftp://bsmcha1.biochem.ucl.ac.uk/pub/procheck/source3_3 VAX/VMS and the ftp://bsmcha1.biochem.ucl.ac.uk/pub/procheck/tar3_3 UNIX systems. -- http://www.public.iastate.edu/~pedro/rt_1.html
PEOPLE
PGPLOT -- Graphics Subroutine Library -- http://astro.caltech.edu/~tjp/pgplot/
PHARMA ALGORITHMS
Polar -- electrochemical simulation and data analysis (http://www.electrochem.net, http://www.DrHuang.com).
PrestoPlot Version 1.16 -- A freely available 2D plotting tool for Win32 Platforms -- http://lancelot.bio.cornell.edu/jason/presto.html
Prospect 2--PROSPECT is a threading-based protein structure prediction system--http://compbio.ornl.gov/structure/prospect2/
PROUS SCIENCE
PyMOL-- Free and unrestricted open-source molecular graphics system -- http://pymol.sourceforge.net/
Q
Q-chem -- ab initio and DFT molecular modeling package http://www.chemistry-software.com/qchem/qchem.htm
Qmol and PrestoPlot--New versions--http://www.mbg.cornell.edu/shalloway/shalloway.html
QUANTUM PHARMACEUTICALS
QUESTEL.ORBIT
R
RASMOL -- http://www.umass.edu/microbio/rasmol
RESCENTRIS
Research Information Systems (Bibliographic) US
RockWare Inc. US
ROYAL SOCIETY OF CHEMISTRY (RSC)
S
Sage Informatics LLC (ChemTK Lite) US
Schrödinger Inc. US
Schrodinger, Inc.'s -- Computational CHemistry Software -- http://www.schrodinger.com/
Science Hypermedia Inc. US
ScienceServe (Software Distributor) DE
Scienomics -- http://www.scienomics.com. Software for Materials R & D, modeling and simulation.
Scientific Computing & Modelling -- http://www.scm.com
Scientific Computing & Modelling NV (SCM) NL
Scientific Software Catalogue -- http://www.scitechint.com/
Scientific Software Inc. (SSI) US
Scientific Software US
SciLetter RU
SciTech International US
SciVision US
Scribner Associates US
Seascape -- computational science company offering software, research consulting and software services -- http://www.seascapelearning.com
Shape Software (Atomic-structure display) UK
Sierra Analytics (Mass spec.) US
SIGMA-ALDRICH
SIMBIOSYS
SimBioSys Inc. CA
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: - molecular modelling toolkits: MoDeST(R), CheVi (R) - applications: Leo, Sprout Chemical Informatics Software product for any chemist: - CLiDE - Chemical Literature Data Extraction
SIMULATIONS PLUS
Simulations Plus US
Sketch & Fetch -- Application of Java to search chem. databases -- http://www.sgi.com/ChemBio/Tripos/WebSketch/
Soft Imaging System GmbH (Scientific Digital Image Analysis) DE
SoftShell US
Solomon Industries Inc. US
SOLUTIONS Software Co. (MSDS) US
Solva Software (MSDS) UK
Spectra Heap CZ
Spectrum Research US
Spot Software Archive DE
SPOTFIRE
SPRINGER SCIENCE+BUSINESS MEDIA
SPS: Simple Queueing System -- https://sourceforge.net/projects/sqs/
SPSS Inc. (Formerly Jandel) US
SQS--is the Simple Queueing System that allows jobs to be run in sequence on a single machine -- https://sourceforge.net/projects/sqs/
StarLIMS US
Statistical Solutions Ltd. IE
StatSoft Inc. US
STC--This program is a UNIX based program that can calculate binding energies using sovent accessible surface area (ASA), and has been shown to be quite precise in certain cases (nothing is good for ALL applications in comp chem!). -- http://www.pence.ualberta.ca/ftp/stc/index.html
STN Databases DE
Sunicom Oy. FI
Sunset Molecular Discovery, LLC -- http://sunsetmolecular.com/ -- WOMBAT-PK and WOMBAT: Pharmacokinetics and BioActivity Databases;ChemGPS: Chemical Global Positioning System
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/
SWISS-PDB VIEWER: http://www.expasy.org/spdbv/
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.obbligato.com/software/swizard/
Symbolic Algebra Package -- Maple -- http://129.97.140.58/
SYMYX TECHNOLOGIES
Synergy Software -- Terminal Emulators -- http://www.synergy.com/
Synoptics Imaging Systems and Solutions UK
Syracuse Research Co. US
SysChem Corp. Inc. US
T
TAYLOR & FRANCIS
Taylor Scheduling Software Inc. US
Tcl/Tk -- WWW resources for Tool Command Language -- http://www.sco.com/Technology/tcl/Tcl.html
Technical Database Services US
Telecation (LIMS) US
TEMIS
TGS - Visual Concepts FR/US
THE EDGE SOFTWARE CONSULTANCY
The Simtel.Net Chemistry Collection US
TheopPrax Research DE
THIEME
Thistle Publishing (MSDS) US
THOMSON SCIENTIFIC
Thru-Put Systems Inc. (Chromatography software) US
TINKER Molecular Modeling Software -- http://dasher.wustl.edu/tinker/
Transient V2.52 -- A new reaction-diffusion equations solver -- http://transient.mkolar.org
Trilogy Environmental UK
TRIPOS
Tripos, Inc. -- software products and services for compound research in pharmaceutical, -- http://www.tripos.com biotechnological, and related organizations worldwide
U
UK PUBMED CENTRAL
Umetrics AB SE
UNICHEM Home Page -- http://www.oxmol.com/prods/unichem/
UNIVIS-2000 -- Molecular Visualization Package from University of Pune. Free for Academia. http://chem.unipune.ernet.in/univis.html
Upstream Solutions CH
V
VEGA
VEGA1.4.3--program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). -- http://www.ddl.unimi.it/
Versal Technologies US
Virtual Chemistry Inc. US
Visual Data (www.visipoint.fi)
VMD Molecular Visualization Software -- http://www.ks.uiuc.edu/Research/vmd/
Vogel Scientific Software Inc. US
W
W.S. Ping Company (Electrochemical software) AU
Wavefunction -- http://www.wavefun.com/
Wavefunction Inc. US
WHATIF - sequence analysis package -- http://www.sander.embl-heidelberg.de/whatif/
Windmill Software Ltd. (Measurement and Control Software) UK
WindowChem US
WinTorg AU
Wolfram Research Inc. US
WOLTERS KLUWER HEALTH
X
Y
Z
Zumatrix Inc. US