Protein Dock Overview
1982: Dock; Kuntz, Irwin D., et al.[1] (Rigid body-shape based)
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| © Kuntz, Irwin D., et al. 1982[1:1] |
In this paper, Kuntz present a way of docking prediction by searching the steric overlap based on the knowing surface structure of 2 proteins. It originally developed by Irwin “Tack” Kuntz and colleagues at the University of California, San Francisco (UCSF), DOCK was initially used for small-molecule docking. However, it laid the foundation for the development of more advanced docking algorithms and software that could handle macromolecular docking.
In the first generation of the Dock, it focus on 2 rigid bodies. It treat 2 proteins as one object. The goal of this program is to fix the 6 degree of freedom (3 transitions and 3 orientations) that determine the best relative position. For achieving this goal, three rules are followed:
- No overlap between 2 proteins
- all hydrogen are pared with N or O within 3.5 Å.
- all ligand atoms within the receptor binding cite.
Dock families:
- 1994: Firstly extend the DOCK into DNA-protein Docking and by screening the Cambridge Crystallographic Database, they find that the protein CC-1065 has high score.[2]
- 1999: DREAM++[3]: It is a extent package for Dock. It use Dock to predict binding and evaluated the interaction and predicts the product, finally search to find the prohibits.
- 2001: DOCK 4.0[4]: It added incremental construction (to sample the internal degrees of freedom of the ligand) and random search. In the Dock4, the ligand is not rigid anymore. Ligands with rotatable-bonds generated multiple conformation by other model.
- 2006: DOCK 5.0[5]:
- anchoring: new scoring functions, sampling methods and analysis tools; energy minimizing was mentioned during the.
- scoring: energy scoring function based on the AMBERL: only intermolecular van der Waals (VDW) and electrostatic components in the function.
- 2009: DOCK 6: Combining techniques to model RNA–small molecule complexes
- 2013: DOCK3.7[6]:
| DOCK4 | DOCK5 |
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Compare to Other Related Tools
Method | Ligand sampling methoda | Receptor sampling methoda | Scoring functionb | Solvation scoringc,d |
|---|---|---|---|---|
DOCK 4/5 | IC | SE | MM | DDD, GB, PB |
FlexX/FlexE | IC | SE | ED | NA |
Glide | CE + MC | TS | MM + ED | DS |
GOLD | GA | GA | MM + ED | NA |
2003: ZDock
ZDock family
- 2003: ZDOCK: An initial-stage protein-docking algorithm
- 2005: M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
2004: ClusPro
ClusPro: a fully automated algorithm for protein–protein docking
2010: Hex
Ultra-fast FFT protein docking on graphics processors
2014: rDock
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids
2018: InterEvDock
Protein-Protein Docking Using Evolutionary Information
Kuntz I D, Blaney J M, Oatley S J, et al. A geometric approach to macromolecule-ligand interactions[J]. Journal of molecular biology, 1982, 161(2): 269-288. ↩︎ ↩︎
Grootenhuis P D J, Roe D C, Kollman P A, et al. Finding potential DNA-binding compounds by using molecular shape[J]. Journal of Computer-Aided Molecular Design, 1994, 8: 731-750. ↩︎
Makino S, Ewing T J A, Kuntz I D. DREAM++: flexible docking program for virtual combinatorial libraries[J]. Journal of computer-aided molecular design, 1999, 13: 513-532. ↩︎
Ewing T J A, Makino S, Skillman A G, et al. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases[J]. Journal of computer-aided molecular design, 2001, 15: 411-428. ↩︎
Moustakas D T, Lang P T, Pegg S, et al. Development and validation of a modular, extensible docking program: DOCK 5[J]. Journal of computer-aided molecular design, 2006, 20: 601-619. ↩︎
Coleman R G, Carchia M, Sterling T, et al. Ligand pose and orientational sampling in molecular docking[J]. PloS one, 2013, 8(10): e75992. ↩︎
Protein Dock Overview
