Wikiomics:Docking toolbox: Difference between revisions
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==Commercial== | ==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.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??== | ||
| Line 26: | Line 26: | ||
* [http://ligand.info/ Ligand.Info] Small-Molecule Meta-Database | * [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://zinc.docking.org/ ZINC] a free database of commercially-available compounds for virtual screening | ||
* [http://lpdb.chem.lsa.umich.edu/ | * [http://lpdb.chem.lsa.umich.edu/ LPDB.] Curated target and ligand structures | ||
* [http://swissdock.vital-it.ch/s3db/index.php | * [http://swissdock.vital-it.ch/s3db/index.php S3DB]Database of manually curated target and ligand structures | ||
==Reviews/Info== | ==Reviews/Info== | ||
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[[Category:Protocol]] | [[Category:Protocol]] | ||
[[Category:In silico]] | [[Category:In silico]] | ||
[[Category:Modelling]] | [[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
