Wikiomics:Docking toolbox: Difference between revisions
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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: | ||
== | ==Commercial== | ||
* | * [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.molsoft.com/docking.html ICM] (docking) | ||
* | * [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 GLIDE] | ||
* [http://accelrys.com/products/materials-studio/ Materials Studio] | |||
*[http://www.arguslab.com/ ArgusLab] | |||
==Free/Semi Free??== | ==Free/Semi Free??== | ||
!! needs verification as of Nov 2006!! | !! needs verification as of Nov 2006!! | ||
* | * [http://autodock.scripps.edu/ AutoDock] | ||
* | * [http://dock.compbio.ucsf.edu/ DOCK] from UCSF . Rigid and Flexible Ligand Docking. | ||
==Reviews== | * [http://gemdock.life.nctu.edu.tw/dock/ GEMDOCK] | ||
* [http://swissdock.vital-it.ch/ SwissDock] | |||
=Ligands databases= | |||
* [http://ligand.info/ Ligand.Info] Small-Molecule Meta-Database | |||
* [http://zinc.docking.org/ ZINC] a free database of commercially-available compounds for virtual screening | |||
* [http://lpdb.chem.lsa.umich.edu/ LPDB.] Curated target and ligand structures | |||
* [http://swissdock.vital-it.ch/s3db/index.php S3DB]Database of manually curated target and ligand structures | |||
==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] | ||
* UCSF docking [http://wiki.compbio.ucsf.edu/wiki/index.php/Main_Page wiki] | |||
=Protein-protein docking= | |||
* [http://zdock.bu.edu/ 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 | |||
*[http://www.loria.fr/~ritchied/hex/ 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. | |||
** [http://www.loria.fr/~ritchied/hex/licence.html HEX] | |||
== Credits == | |||
{{credits}} | |||
* [[User:Darked|Darek Kedra]] wrote this tutorial | |||
<!-- other contributors, put yourself here --> | |||
[[Category:Protocol]] | |||
[[Category:In silico]] | |||
[[Category:Modelling]] | |||
[[Category:Structure]] | |||
Latest revision as of 18:39, 29 December 2011
Following programs are used for docking small molecules into protein pockets/active sites:
Commercial
- FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [1]
- GOLD
- ICM (docking)
- GLIDE
- Materials Studio
- ArgusLab
Free/Semi Free??
!! needs verification as of Nov 2006!!
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
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]
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.
Credits
- Darek Kedra wrote this tutorial
