DOCK explained
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| Author: | Brian K. Shoichet, David A. Case, Robert C.Rizzo |
| Developer: | University of California, San Francisco |
| Latest Release Version: | 3 series: 3.7; 6 series: 6.7 |
| Programming Language: | DOCK 3: Fortran, C
DOCK 6: C++, C, Fortran 77 |
| Operating System: | DOCK 3: source code
DOCK 6: Linux, macOS, Windows |
| Platform: | x86, x86-64 |
| Size: | 100 MB |
| Language: | English |
| Genre: | Molecular docking |
| License: | Proprietary freeware academic, commercial
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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 codevelopers of DOCK.
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 (v3.5-3.7).[5] [6]
A molecular dynamics engine was implemented into DOCK v6 by David A. Case's Group in the scoring function AMBER score. This ability accounts for receptor flexibility and allows for rank ordering by energetic ensembles in the docking calculations.[4]
See also
Notes and References
- Kuntz . ID . Blaney . JM . Oatley . SJ . Langridge . R . Ferrin . TE . A geometric approach to macromolecule-ligand interactions . Journal of Molecular Biology . 161 . 2 . 269–88 . 1982 . 7154081 . 10.1016/0022-2836(82)90153-X.
- Ewing . TJ . Makino . S . Skillman . AG . Kuntz . ID . DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases . Journal of Computer-aided Molecular Design . 15 . 5 . 411–28 . 2001 . 11394736 . 10.1023/A:1011115820450. 2001JCAMD..15..411E . 5553209 .
- Moustakas . DT . Lang . PT . Pegg . S . Pettersen . E . Kuntz . ID . Brooijmans . N . Rizzo . RC . Development and validation of a modular, extensible docking program: DOCK 5 . Journal of Computer-aided Molecular Design . 20 . 10–11 . 601–19 . 2006 . 17149653 . 10.1007/s10822-006-9060-4. 2006JCAMD..20..601M . 24495648 .
- Lang . PT . Brozell . SR . Mukherjee . S . Pettersen . EF . Meng . EC . Thomas . V . Rizzo . RC . Case . DA . James . TL . Kuntz . I. D. . DOCK 6: Combining techniques to model RNA–small molecule complexes . RNA . 15 . 6 . 1219–30 . 2009 . 19369428 . 2685511 . 10.1261/rna.1563609 . 8.
- Lorber . DM . Shoichet . BK . Flexible ligand docking using conformational ensembles . Protein Sci . 7 . 4 . 938–950 . 1998 . 9568900 . 2143983 . 10.1002/pro.5560070411.
- Lorber . DM . Shoichet . BK . Hierarchical Docking of Databases of Multiple Ligand Conformations . Curr Top Med Chem . 5 . 8 . 739–49 . 2005 . 16101414 . 10.2174/1568026054637683 . 1364474.
