DOCK

The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz's Group, and was the first docking program.^[1] DOCK uses geometric algorithms to predict the binding modes of small molecules.^[2][3][4] 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),^[2] and hierarchical docking of databases (v3.5-3.7).^[5][6]

A molecular dynamics 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.^[4]

See also

• AutoDock
• Molecular modeling
• List of software for molecular mechanics modeling

References

1. Kuntz, ID; Blaney, JM; Oatley, SJ; Langridge, R; Ferrin, TE (1982). "A geometric approach to macromolecule-ligand interactions". Journal of Molecular Biology 161 (2): 269–88. doi:10.1016/0022-2836(82)90153-X. PMID 7154081.
2. Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID (2001). "DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases". Journal of computer-aided molecular design 15 (5): 411–28. doi:10.1023/A:1011115820450. PMID 11394736.
3. Moustakas, DT; Lang, PT; Pegg, S; Pettersen, E; Kuntz, ID; Brooijmans, N; Rizzo, RC (2006). "Development and validation of a modular, extensible docking program: DOCK 5". Journal of computer-aided molecular design 20 (10–11): 601–19. doi:10.1007/s10822-006-9060-4. PMID 17149653.
4. Lang, PT; Brozell, SR; Mukherjee, S; Pettersen, EF; Meng, EC; Thomas, V; Rizzo, RC; Case, DA; et al. (2009). "DOCK 6: Combining techniques to model RNA–small molecule complexes". RNA 15 (6): 1219–30. doi:10.1261/rna.1563609. PMC 2685511. PMID 19369428.
5. Lorber, DM; Shoichet, BK (1998). "Flexible ligand docking using conformational ensembles". Protein Sci 7 (4): 938–950. doi:10.1002/pro.5560070411. PMC 2143983. PMID 9568900.
6. Lorber, DM; Shoichet, BK (2005). "Hierarchical Docking of Databases of Multiple Ligand Conformations". Curr Top Med Chem 5 (8): 739–49. doi:10.2174/1568026054637683. PMC 1364474. PMID 16101414.