Wikiomics:Docking toolbox

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Following programs are used for docking small molecules into protein pockets/active sites:
Following programs are used for docking small molecules into protein pockets/active sites:
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==Comercial==
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==Commercial==
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* FlexX [http://www.biosolveit.de/FlexX/] (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [http://www.cmbi.ru.nl/edu/bioinf4/thu-Prac/screening/screenings.shtml]  $$$
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* [http://www.biosolveit.de/FlexX/ FlexX ] (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [http://www.cmbi.ru.nl/edu/bioinf4/thu-Prac/screening/screenings.shtml]  $$$
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* GOLD [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/] $$$
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* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD ] $$$
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* ICM (docking) [http://www.molsoft.com/docking.html] $$$
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* [http://www.molsoft.com/docking.html ICM] (docking)$$$
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* GLIDE [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6] $$$
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* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 GLIDE] $$$
==Free/Semi Free??==
==Free/Semi Free??==
!! needs verification as of Nov 2006!!
!! needs verification as of Nov 2006!!
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* AutoDock [http://autodock.scripps.edu/]
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* [http://autodock.scripps.edu/ AutoDock]
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* UCSF DOCK [http://dock.compbio.ucsf.edu/]
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* [http://dock.compbio.ucsf.edu/ DOCK] from UCSF . Rigid and Flexible Ligand Docking.
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* GEMDOCK [http://gemdock.life.nctu.edu.tw/dock/]
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* [http://gemdock.life.nctu.edu.tw/dock/ GEMDOCK]
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=Ligands databases=
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* [http://ligand.info/ Ligand.Info] Small-Molecule Meta-Database
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* [http://zinc.docking.org/ ZINC] a free database of commercially-available compounds for virtual screening
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==Reviews==
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==Reviews/Info==
* Sperandio O, Miteva MA, Delfaud F, Villoutreix  Receptor-based computational screening of compound databases: the main docking-scoring engines.Curr Protein Pept Sci. 2006 Oct;7(5):369-93.
* Sperandio O, Miteva MA, Delfaud F, Villoutreix  Receptor-based computational screening of compound databases: the main docking-scoring engines.Curr Protein Pept Sci. 2006 Oct;7(5):369-93.
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* very good review by Aatu Kaapro Janne Ojanen from 2002: [http://www.lce.hut.fi/teaching/S-114.500/2002/Protdock.pdf]
* very good review by Aatu Kaapro Janne Ojanen from 2002: [http://www.lce.hut.fi/teaching/S-114.500/2002/Protdock.pdf]
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* UCSF docking [http://wiki.compbio.ucsf.edu/wiki/index.php/Main_Page wiki]
== Credits ==
== Credits ==

Revision as of 07:40, 18 January 2008



Following programs are used for docking small molecules into protein pockets/active sites:

Contents

Commercial

  • FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [1] $$$
  • GOLD $$$
  • ICM (docking)$$$
  • GLIDE $$$

Free/Semi Free??

!! needs verification as of Nov 2006!!

  • AutoDock
  • DOCK from UCSF . Rigid and Flexible Ligand Docking.

Ligands databases

  • Ligand.Info Small-Molecule Meta-Database
  • ZINC a free database of commercially-available compounds for virtual screening

Reviews/Info

  • Sperandio O, Miteva MA, Delfaud F, Villoutreix Receptor-based computational screening of compound databases: the main docking-scoring engines.Curr Protein Pept Sci. 2006 Oct;7(5):369-93.
  • Muegge, M Rarey - mall molecule docking and scoring Reviews in Computational Chemistry, Dec 2001 [2]
  • very good review by Aatu Kaapro Janne Ojanen from 2002: [3]
  • UCSF docking wiki

Credits

Template:Credits

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