The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz

Irwin "Tack" Kuntz

This article about Molecular modelling is a stub. You can help Wikipedia by [/w/index.php?stub&title=&action=edit expanding it].Irwin D. Kuntz is an important figure in the field of computer-aided drug design and molecular modeling. He is a pioneer in the development and conception of the area of...

's Group, and was the first docking program. DOCK uses geometric algorithms to predict the binding modes of small molecules. Brian K. Shoichet, David A. Case, and Robert C.Rizzo are co-developers of the DOCK program.

Two versions of the docking program are actively developed DOCK 6 and DOCK 3.

Ligand sampling methods used by the program DOCK include.

• Rigid docking: shape matching, uses spheres placed in the pocket and performs bipartite matching between those spheres and the molecule (all versions).
• Flexible ligand is accounted for using the following methods: an algorithm called anchor and grow (v4-v6), and hierarchical docking of databases (v3.5).

A molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

engine was implemented into DOCK v6 by David A. Case's Group in the scoring function amber score. This capability accounts for receptor flexibility and allows for rank ordering by energetic ensembles in the docking calculations.

External links

• manual page: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm

• web page: http://dock.compbio.ucsf.edu/

• dock wiki: http://wiki.bkslab.org/index.php/Main_Page

• Rizzo lab wiki: http://ringo.ams.sunysb.edu