Hydrophobic docking: a proposed enhancement to molecular recognition techniques
- PMID: 7731951
- DOI: 10.1002/prot.340200405
Hydrophobic docking: a proposed enhancement to molecular recognition techniques
Abstract
In the classical procedures for predicting the structure of protein complexes two molecules are brought in contact at multiple relative positions, the extent of complementarity (geometric and/or energy) at the surface of contact is assessed at each position, and the best fits are retrieved. In view of the higher occurrence of hydrophobic groups at contact sites, their contribution results in more intermolecular atom-atom contacts per unit area for correct matches than for false positive fits. The hydrophobic groups are also potentially less flexible at the surface. Thus, from a practical point of view, a partial representation of the molecules based on hydrophobic groups should improve the quality of the results in finding molecular recognition sites, as compared to full representation. We tested this proposal by applying the idea to an existing geometric fit procedure and compared the results obtained with full vs. hydrophobic representations of molecules in known molecular complexes. The hydrophobic docking yielded distinctly higher signal-to-noise ratio so that the correct match is discriminated better from false positive fits. It appears that nonhydrophobic groups contribute more to false matches. The results are discussed in terms of their relevance to molecular recognition techniques as compared to energy calculations.
Similar articles
-
Hydrophobic complementarity in protein-protein docking.Proteins. 2004 Jul 1;56(1):130-42. doi: 10.1002/prot.20145. Proteins. 2004. PMID: 15162493
-
Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions.Proteins. 2007 Feb 1;66(2):388-98. doi: 10.1002/prot.21122. Proteins. 2007. PMID: 17094116
-
Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking.J Mol Biol. 1996 Nov 22;264(1):199-210. doi: 10.1006/jmbi.1996.0634. J Mol Biol. 1996. PMID: 8950278
-
Flexible protein-protein docking.Curr Opin Struct Biol. 2006 Apr;16(2):194-200. doi: 10.1016/j.sbi.2006.02.002. Epub 2006 Feb 17. Curr Opin Struct Biol. 2006. PMID: 16488145 Review.
-
On proteins, grids, correlations, and docking.C R Biol. 2004 May;327(5):409-20. doi: 10.1016/j.crvi.2004.03.006. C R Biol. 2004. PMID: 15255472 Review.
Cited by
-
Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules. 2024 Oct 1;14(10):1245. doi: 10.3390/biom14101245. Biomolecules. 2024. PMID: 39456178 Free PMC article. Review.
-
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annu Rev Biophys. 2023 May 9;52:183-206. doi: 10.1146/annurev-biophys-102622-084607. Epub 2023 Jan 10. Annu Rev Biophys. 2023. PMID: 36626764 Free PMC article. Review.
-
Protein-Protein Interactions in Translesion Synthesis.Molecules. 2021 Sep 13;26(18):5544. doi: 10.3390/molecules26185544. Molecules. 2021. PMID: 34577015 Free PMC article. Review.
-
Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.RNA. 2018 Sep;24(9):1183-1194. doi: 10.1261/rna.065896.118. Epub 2018 Jun 21. RNA. 2018. PMID: 29930024 Free PMC article.
-
Using 3dRPC for RNA-protein complex structure prediction.Biophys Rep. 2016;2(5):95-99. doi: 10.1007/s41048-017-0034-y. Epub 2017 Feb 10. Biophys Rep. 2016. PMID: 28317012 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
