Wikiomics:Docking toolbox

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (+ credits)
Current revision (20:39, 29 December 2011) (view source)
m
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
{{stub}}
{{stub}}
 +
 +
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:
-
==Comercial==
+
==Commercial==
-
* 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]  $$$
+
* [http://www.biosolveit.de/FlexX/ FlexX ] (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [http://www.cmbi.ru.nl/edu/bioinf4/thu-Prac/screening/screenings.shtml]   
-
* GOLD [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/] $$$
+
* [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD ]
-
* ICM (docking) [http://www.molsoft.com/docking.html] $$$
+
* [http://www.molsoft.com/docking.html ICM] (docking)
-
* GLIDE [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6] $$$
+
* [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!!
-
* AutoDock [http://autodock.scripps.edu/]
+
* [http://autodock.scripps.edu/ AutoDock]
-
* UCSF DOCK [http://dock.compbio.ucsf.edu/]
+
* [http://dock.compbio.ucsf.edu/ DOCK] from UCSF . Rigid and Flexible Ligand Docking.  
-
* GEMDOCK [http://gemdock.life.nctu.edu.tw/dock/]
+
-
==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.
Line 23: Line 35:
* 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 ==
Line 30: Line 52:
* [[User:Darked|Darek Kedra]] wrote this tutorial
* [[User:Darked|Darek Kedra]] wrote this tutorial
<!-- other contributors, put yourself here -->
<!-- other contributors, put yourself here -->
 +
 +
[[Category:Protocol]]
 +
[[Category:In silico]]
 +
[[Category:Modelling]]
 +
[[Category:Structure]]

Current revision



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

Contents

Commercial

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

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

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

Template:Credits

Personal tools