Wiki‎ > ‎

List of Computational Chemistry Software

posted Mar 19, 2013, 11:33 AM by Dong Xu   [ updated Mar 19, 2013, 11:39 AM ]
https://docs.google.com/file/d/0BwAR2nWq4Z0eTXpjaGZ3cnVMMFU/edit?usp=sharing
===========================================

Databases

  1. Compounds

    ACD Symyx www.symyx.com 9, 14

    ChemBridge ChemBridge www.chembridge.com 12, 14, 15 ChemDiv ChemDiv www.chemdiv.com 14

    ChemDB University of

    California, Irvine

    ChemSpider Royal Society of Chemistry

    cdb.ics.uci.edu 1

    www.chemspider.com 1, 2

    CSD CCDC www.ccdc.cam.ac.uk/pro- 4 ducts/csd

    eMolecules eMolecules, Inc. www.emolecules.com 1

    GDB-13 University of Berne www.dcb-server.unibe.ch/ groups/reymond/gdb/

    home.html

    1

    (Continued)


    Virtual Screening. Edited by C. Sotriffer

    Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

    ISBN: 978-3-527-32636-5

    Type Software name Developed at or

    provided by

    Reference/ Web site

    Cited in Chapter


    InterBioScreen InterBioScreen www.ibscreen.com 14

    Maybridge Maybridge www.maybridge.com 14, 15

    NCI/DTP National Cancer Institute

    dtp.nci.nih.gov/docs/ 3d_database/Structural_

    information/structural_ data.html

    9, 12, 14,

    15

    SPECS Specs www.specs.net 12

    SureChem SureChem Inc. www.surechem.org 1

    VEHICLe UCB Celltech J. Med. Chem. 2009, 52, 2952. 1

    ZINC UCSF zinc.docking.org 1, 2, 11, 12,

    14

  2. Interactions and targets

AurSCOPE Aureus Pharma www.aureus-pharma.com 1

BioPrint Cerep www.cerep.fr 1

ChEMBLdb EMBL-EBI www.ebi.ac.uk/chembldb 1, 5

ChemBank Broad Institute chembank. 1

broadinstitute.org

DIP University of

California, Los Angeles

dip.doe-mbi.ucla.edu 16

DOCKGROUND University of Kansas dockground. 16

bioinformatics.ku.edu/ index.shtml

DOMINE University of Texas at Dallas

domine.utdallas.edu/ 16

cgi-bin/Domine

DrugBank University of Alberta www.drugbank.ca 1

DUD University of California, San

Francisco

dud.docking.org 2, 7, 10

MDDR MDL www.symyx.com 2, 12, 14 MINT University of Rome mint.bio.uniroma2.it/mint 16

MUV University of Braunschweig

www.pharmchem.tu-bs.de/ 5 lehre/baumann/MUV.html

PDB RCSB, Rutgers, UCSD

www.pdb.org 1, 4, 7, 10,

12, 14, 16

PDBbind University of Michi- gan and Shanghai

Institute of Organic Chemistry

www.pdbbind.org and www. pdbbind.org.cn

7, 10

PIBASE Janelia Farm pibase.janelia.org 16

PRISM Koc University, Istanbul

prism.ccbb.ku.edu.tr 16

PROTCOM Clemson University Nucleic Acids Res. 2007, 16

35, D575.

PubChem NIH, NCBI pubchem.ncbi.nlm.nih.gov 1, 5

ReliBase CCDC relibase.ccdc.cam.ac.uk 4, 7

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

SCORPIO University of London scorpio.biophysics.ismb.lon. 10

ac.uk

WOMBAT Sunset Molecular www.sunsetmolecular.com 1, 5 World Drug Index Thomson Reuters thomsonreuters.com 5, 15


Chemoinformatic tools and workow toolkits

ChemAxon ChemAxon www.chemaxon.com 6

Filter OpenEye www.eyesopen.com 6

Inforsense Inforsense www.inforsense.com 2

KNIME KNIME.com GmbH www.knime.org 2

LigPrep Schrodinger www.schrodinger.com 16

OEChem OpenEye www.eyesopen.com 2

OpenBabel OpenBabel commu- nity project

openbabel.org 2

PipelinePilot Accelrys accelrys.com 2, 5, 6, 13

Taverna myGrid taverna.sourceforge.net 2

Topomers (dbtop) Tripos tripos.com 13

Similarity analysis

ACCS-FP University of Bonn

ChemMedChem 11

2008, 3, 67.

ChemGPS University of Uppsala chemgps.bmc.uu.se 1

Dragon TALETE srl www.talete.mi.it 1

DynaMAD University of Bonn J. Chem. Inf. Model. 2006, 46, 11

1623.

EON OpenEye www.eyesopen.com 13

Fieldscreen Cresset www.cresset-bmd.com 13

FLAP Molecular Discovery J. Chem. Inf. Model. 2007, 47, 279.

5, 12

FTrees, FTrees-FS BioSolveIT www.biosolveit.de 1, 3

GRIND (Almond/ Pentacle)

Molecular Discovery www.moldiscovery.com 12

Meqi Pannanugget

Consulting

www.pannanugget.com 1

MoBSS Pzer J. Chem. Inf. Model. 2009, 49, 1

745.

ROCS OpenEye www.eyesopen.com 3, 12, 13

Scaffold Hunter TU Dortmund/MPI

Dortmunt

www.scaffoldhunter.com 1

Volsurf Molecular Discovery www.moldiscovery.com 12


Conformer generation

Caesar Accelrys accelrys.com 6

Concord Tripos tripos.com 13, 14

Corina Molecular Networks www.molecular- 6

networks.com

DS Catalyst CONFIRM

Accelrys accelrys.com 5, 6

(Continued)

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

Omega OpenEye www.eyesopen.com 5, 6

ROTATE Molecular Networks www.molecular- 5

networks.com


Pharmacophore modeling

DS Catalyst Accelrys accelrys.com 5, 12, 13,

15

GALAHAD Tripos tripos.com 5

GASP Tripos tripos.com 5

LigandScout inte:ligand www.inteligand.com 5, 10, 15

MOE Chemical Computing Group

www.chemcomp.com 5, 13

PHASE Schrodinger www.schrodinger.com 5, 12

UNITY Tripos tripos.com 5, 10,

1214


De novo design

BREED Chemical Computing Group

www.chemcomp.com 17

CCLD University of Zurich J. Comp. Aided Mol. Des. 1996, 17

10, 372.

GANDI University of Zurich www.biochem-caisch.uzh. 17

ch/download

HOOK Harvard University Proteins 1994, 19, 199. 17

LEA3D University of Nice bioinfo.ipmc.cnrs.fr/lea. 17

html

LUDI Accelrys accelrys.com 12, 17

PRO_ligand Proteus Molecular Design

Skelgen De Novo

Pharmaceuticals

J Comp. Aided Mol. Des. 1995, 17

9, 13.

www.denovopharma.com/ 17 page2.asp

Protein analysis (binding sites, exibility, hot spots, interfaces, water sites, etc.)

Chimera University of California, San

Francisco

www.cgl.ucsf.edu/chimera 16

Consolv Michigan State University

www.bch.msu.edu/

rv kuhn/software/consolv

4, 10

CS-Map Boston University Proteins 2003, 51, 340. 10

DFprot Centro de Investiga- ciones Biol,ogicas

sbg.cib.csic.es/Software/ 16

DFprot

Electron Density

Server

University of Uppsala eds.bmc.uu.se/eds/ 4, 10

FoldX EMBL foldx.crg.es 10, 16

GRID Molecular Discovery www.moldiscovery.com 4, 5, 10, 15 Harmony NCBS, Bangalore caps.ncbs.res.in/harmony 14

HINT eduSoft www.edusoft-lc.com 4, 10

MCSS Accelrys accelrys.com 17

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter


Mogul CCDC www.ccdc.cam.ac.uk/pro- 4 ducts/csd_system/mogul/

Molprobity Duke University molprobity.biochem.duke. 4

edu

MRC University of

California, San Diego

abagyan.ucsd.edu/MRC 16

ODA MolSoft www.molsoft.com/oda.html 16

PIER University of

California, San Diego

abagyan.ucsd.edu/PIER 16

PPI-Pred University of Leeds bmbpcu36.leeds.ac.uk/ 16

ppi_pred

PQS EMBL/EBI www.ebi.ac.uk/pdbe/pqs/ 4

PROCHECK EMBL/EBI www.biochem.ucl.ac.uk/

rv roman/procheck/ procheck.html

4, 14

PROFACE Bose Institute, Kolkata

PROMATE Weizmann Institute of Science

resources.boseinst.ernet.in/ 16 resources/bioinfo/interface

bioinfo.weizmann.ac.il/ 16

promate

PROTORP University of Sussex www.bioinformatics. 16

sussex.ac.uk/protorp

Q-siteFinder University of Leeds www.modelling.leeds.ac.uk/ 16

qsitender

Relibase, Waterbase CCDC relibase.ccdc.cam.ac.uk 4, 7

Robetta University of Washington

robetta.bakerlab.org 16

SuperStar CCDC www.ccdc.cam.ac.uk/pro-

ducts/life_sciences/ superstar/

4, 10

SURFNET University College London

www.biochem.ucl.ac.uk/ 16

rv roman/surfnet/ surfnet.html

UniProt UniProt Consortium www.uniprot.org 4

VMD University of Illinois at Urbana-

Champaign

www.ks.uiuc.edu/Research/ 16 vmd

Watermap Schrodinger www.schrodinger.com 10

WaterScore University of Cam- bridge/De Novo

Pharmaceuticals

J. Mol. Model. 2003, 9, 172. 4, 10

WHAT_CHECK CMBI swift.cmbi.ru.nl/gv/ 4

whatcheck/

Homology modeling

CODA, FREAD, PETRA

Tripos tripos.com 14


Type

Software name

Developed at or provided by

Reference/ Web site

Cited in Chapter


COILS


MOBILE

EMBnet


University of

www.ch.embnet.org/soft- ware/COILS_form.html

J. Mol. Biol. 2003, 334, 327.

14


14



Modeller

Marburg

University of


salilab.org/modeller


14



MOE

California, San

Francisco

Chemical Computing


www.chemcomp.com


2, 14



PLOP

Group

University of


www.jacobsonlab.org


14



PSIPRED

California, San

Francisco University College


bioinf.cs.ucl.ac.uk/psipred


14



SCWRL

London

Fox Chase Cancer


dunbrack.fccc.edu/scwrl4


15



Sybyl Biopolymer

Center

Tripos


tripos.com


14


Whatif

CMBI

swift.cmbi.kun.nl/whatif/

14

MD S

imulations

Amber

UCSF, Scripps

ambermd.org

6, 7, 9


CHARMM


Gromacs

Harvard University/

Accelrys University of

www.charmm.org


www.gromacs.org

6, 7, 17


14



Groningen



Docking

ADAM IMMD, Toyko Proteins 2006, 63, 878. 8

ADDock Biodelight Biotech Inc.

ASEDock Tokai University School of Medicine

www.biodelight.com.tw/ 6

English

J. Chem. Inf. Model. 2008, 48, 6

583.

Autodock The Scripps Research

Institute

autodock.scripps.edu 6, 9, 10, 14,

15

CDOCKER Accelrys accelrys.com 9

ClusPro Boston University nrc.bu.edu/cluster 16

CombiDOCK University of California, San

Francisco

J. Comp.-Aided Mol. Des. 1

1998, 12, 597.

CombiGlide Schrodinger www.schrodinger.com 1

DOCK University of California, San

Francisco

dock.compbio.ucsf.edu 6, 7, 9, 12,

14, 16

DREAM þþ University of California, San

Francisco

J. Comp.-Aided Mol. Des. 1

1999, 13, 513.

eHiTS SimBioSys www.simbiosys.ca 6

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

EUDOC Mayo Foundation for Medical

Education and Research

  1. Comput. Chem. 2001, 22, 12

    1750.

    FITTED McGill University/ Forecaster

    tted.ca 6, 10

    FlexE BioSolveIT www.biosolveit.de 6, 12, 15 FlexNovo BioSolveIT www.biosolveit.de 1

    FlexScreen BioSolveIT www.biosolveit.de 6, 8

    FlexX BioSolveIT www.biosolveit.de 3, 6, 810,

    12, 14, 17

    FlexXC BioSolveIT www.biosolveit.de 1

    FlexX-Pharm BioSolveIT www.biosolveit.de 6, 14

    FLIPDock The Scripps Research Institute

    ipdock.scripps.edu 6, 8

    FRED OpenEye www.eyesopen.com 6, 10, 14

    FRODOCK Centro de Investigaciones

    Biol,ogicas

    FTDock Imperial College London

    GasDock Dalian University of Technology

    sbg.cib.csic.es/Software/ 16

    FRODOCK

    www.sbg.bio.ic.ac.uk/ 16

    docking

    Bioorg. Med. Chem. Lett. 2004, 12

    14, 4671.

    GlamDock Chil2 www.chil2.de 6

    Glide Schrodinger www.schrodinger.com 6, 9, 10,

    12, 1417

    GOLD CCDC www.ccdc.cam.ac.uk/pro- ducts/life_sciences/gold


    GRAMM-X University of Kansas vakser.bioinformatics.ku.

    edu/resources/gramm/ grammx

    Haddock University of Utrecht haddock.chem.uu.nl/

    services/HADDOCK/ haddockservereasy.html

    4, 6, 7, 9,

    10, 12, 14,

    15, 17

    16


    16

    Hex INRIA www.loria.fr/rvritchied/hex 14, 16

    ICM MolSoft www.molsoft.com 6, 12, 14,

    16

    ISE-dock Hebrew University of Jerusalem

    Proteins 2008, 71, 1373. 6

    LibDock Accelrys accelrys.com 14

    Ligandt Accelrys accelrys.com 14

    LIGIN Weizmann

    Institute of Science

    MOE Chemical

    Computing Group

    Proteins 1996, 25, 120. 12

    www.chemcomp.com 14, 15

    Type Software name Developed at or

    provided by

    Reference/ Web site

    Cited in Chapter

    MolFit Weizmann

    Institute of Science

    www.weizmann.ac.il/ 16

    Chemical_Research_ Support//molt

    PatchDock Tel-Aviv University bioinfo3d.cs.tau.ac.il/ 16

    PatchDock

    PLANTS University of Konstanz

    www.tcd.uni-konstanz.de/ 6 research/plants.php

    Pso@autodock University of Leipzig biophys.biow.uni-

    leipzig.de/ psoatautodock.html

    QXP/FLO Colin McMartin J. Comp.-Aided Mol. Des.

    1997, 11, 333.

    6


    10, 12

    rDock York Structural Biol- ogy Laboratory

    RosettaDock Johns Hopkins

    University

    www.ysbl.york.ac.uk/rDock 12


    rosettadock.graylab.jhu.edu 16

    SEED, FFLD University of Zurich www.biochem-caisch.uzh. 17

    ch

    SKE-DOCK Kitasato University www.pharm.kitasato-u.ac.jp/ 16

    bmd/les/SKE_ DOCK.html

    SLIDE Michigan State University

    www.bch.msu.edu/

    rv kuhn/software/slide

    810

    Sodock National Chiao Tung University

    iclab.life.nctu.edu.tw/sodock 6

    Surex Tripos tripos.com 6, 12, 14

    ZDOCK Boston University zdock.bu.edu 16

    Scoring functions (SF)

    1. Empirical SF

      AIScore Raub et al., J. Chem. Inf. Model. 2008, 48, 1492. 7

      AutoDock3 SF Morris et al., J. Comput. Chem. 1998, 19, 1639. (7)

      AutoDock4 SF Huey et al., J. Comput. Chem. 2007, 28, 1145. (7)

      ChemScore Eldridge et al., J. Comp.-Aided Mol. Des. 1997, 11, 425. 7, 12, 14

      eHITS SF Zsoldos et al., J. Mol. Struct. Theochem. 2003, 7

      666667, 659.

      FlexX SF Rarey et al., J. Mol. Biol. 1996, 261, 470. (7)

      Fresno Rognan et al., J. Med. Chem. 1999, 42, 4650. (7)

      GlideScore/GlideXP Friesner et al., J. Med. Chem. 2006, 49, 6177. 7, 16

      Giordanetto’s SF Giordanetto et al., J. Chem. Inf. Comput. Sci. 2004, 44, 7 882.

      Jain’s SF Jain, J. Comp. Aided Mol. Des. 1996, 10, 427. (7)

      LigScore Krammer et al., J. Mol. Graph. Model. 2005, 23, 395. (7)

      PLP Gehlhaar et al., Chem. Biol. 1995, 2, 317. 6, 7

      RankScore Moitessier et al., J. Med. Chem. 2006, 49, 5885. 7

      SCORE Wang et al., J. Mol. Model. 1998, 4, 379. (7)

      SCORE 3.0 Pei et al., Proteins 2006, 62, 934. (7)

      Type Software name Developed at or

      provided by

      Reference/ Web site

      Cited in Chapter


      SCORE1 Boehm, J. Comp. Aided Mol. Des. 1994, 8, 243. (7)

      SCORE2 Boehm, J. Comp. Aided Mol. Des. 1998, 12, 309. (7)

      ScreenScore Stahl et al., J. Med. Chem. 2001, 44, 1035. (7)

      SFCscore Sotriffer et al., Proteins 2008, 73, 395. 7

      SIE (FF) Naim, J. Chem. Inf. Model. 2007, 47, 122. (7)

      SLIDE SF Schnecke et al., Perspect. Drug Discov. Des. 2000, 20, 7 171.

      Surex-Dock Pham et al., J. Med. Chem. 2006, 49, 5856. 7

      X-Score Wang et al., J. Comp.-Aided Mol. Des. 2002, 16, 11. (7)

      ASP

      Mooij et al., Proteins 2005, 61, 272.

      7

      BLEEP

      Mitchell et al., J. Comput. Chem. 1999, 20, 1165.

      7

      DFIRE

      Zhang et al., J. Med. Chem. 2005, 48, 2325.

      (7)

      DrugScorePDB

      Gohlke et al., J. Mol. Biol. 2000, 295, 337.

      7

      DrugScoreCSD

      Velec et al., J. Med. Chem. 2005, 48, 6296.

      7

      ITScore

      Huang et al., J. Comput. Chem. 2006, 27, 1866.

      (7)

      M-Score

      Yang et al., J. Med. Chem. 2006, 49, 5903.

      7

      PMF

      Muegge, J. Med. Chem. 2006, 49, 5895.

      7

      SMoG

      Ishchenko et al., J. Med. Chem. 2002, 45, 2770.

      7

      Other approaches



      AFMoC

      Gohlke et al., J. Med. Chem. 2002, 45, 4153.

      7

      AutoShim

      Martin et al., J. Chem. Inf. Model. 2008, 48, 861.

      7

      BBCS

      Fukunishi et al., J. Chem. Inf. Model. 2008, 48, 988.

      7

      COMBINE

      Ortiz et al., J. Med. Chem. 1995, 38, 2681.

      7

      CScore

      Clark et al., J. Mol. Graph. Model. 2002, 20, 281.

      14

      GFScore

      Betzi et al., J. Chem. Inf. Model. 2006, 46, 1704.

      7

      HINT

      Cozzini et al., J. Med. Chem. 2002, 45, 2469.

      4, 7, 10

      HYDE

      Reulecke et al., ChemMedChem 2008, 3, 885.

      7

      0

      LIE Aqvist et al., Protein Eng. 1994, 7, 385. 6, 7, 10,

      LIECE

      Huang et al., J. Med. Chem. 2004, 47, 5791.

      7, 17

      MM-GBSA

      Huang et al., J. Chem. Inf. Model. 2006, 46, 243.

      7, 9, 10

      MM-PBSA

      Kollman et al., Acc. Chem. Res. 2000, 33, 889.

      7, 9, 10

      ROTA

      Hartmann et al.,, Proteins 2009, 74, 712.

      14

      SeleX-CS

      Bar-Haim et al., J. Chem. Inf. Model. 2009, 49, 623.

      7

      SIFt

      Deng et al., J. Med. Chem. 2004, 47, 337.

      1, 57

      SSM

      Teramoto et al., J. Chem. Inf. Model. 2007, 47, 1858.

      7

      TOP

      Seifert, J. Comp. Aided Mol. Des. 2009, 23, 633.

      7

      TScore

      Matter et al., J. Med. Chem. 2005, 48, 3290.

      7

    2. Knowledge-based SF


(C)


17


Miscellaneous

AMSOL (solvation free energies)


University

of Minnesota


comp.chem.umn.edu/amsol 12

DAIM (molecule decomposition)

University of Zurich www.biochem-caisch.uzh. 17

ch

Fragment RECAP method (molecule

fragmentation)

ChemAxon chemaxon.com 1, 3


Comments