Difference between revisions of "Wikiomics:Docking toolbox"

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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]  $$$
* [http://www.biosolveit.de/FlexX/ FlexX ] (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [http://www.cmbi.ru.nl/edu/bioinf4/thu-Prac/screening/screenings.shtml]   
* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD ] $$$
* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD ]
* [http://www.molsoft.com/docking.html ICM] (docking)$$$
* [http://www.molsoft.com/docking.html ICM] (docking)
* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 GLIDE] $$$
* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 GLIDE]  
* [http://accelrys.com/products/materials-studio/ Materials Studio]
* [http://accelrys.com/products/materials-studio/ Materials Studio]
*[http://www.arguslab.com/ ArgusLab]$$$
*[http://www.arguslab.com/ ArgusLab]
==Free/Semi Free??==
==Free/Semi Free??==
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[[Category:In silico]]
[[Category:In silico]]
[[Category:Data analysis]]

Latest revision as of 18:39, 29 December 2011

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


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
  • LPDB. Curated target and ligand structures
  • S3DBDatabase of manually curated target and ligand structures


  • 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

Protein-protein docking

  • ZDOCK rigid docking, "Fast Fourier Transform based protein docking program. It takes two PDB files and outputs the predicted structure of their complex" See also: http://wiki.bioinformatics.org/ZDOCK @bioinformatics.org]
    • M-ZDOCK
    • ZRANK
    • RDOCK
  • HEX Hex is an interactive protein docking and molecular superposition program.It takes protein and DNA PDB file format and also read small-molecule SDF files.