Premium
Hydrophobic docking: A proposed enhancement to molecular recognition techniques
Author(s) -
Vakser Ilya A.,
Aflalo Claude
Publication year - 1994
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340200405
Subject(s) - complementarity (molecular biology) , intermolecular force , molecule , hydrophobic effect , representation (politics) , chemistry , molecular recognition , docking (animal) , computer science , artificial intelligence , biological system , chemical physics , medicine , biochemistry , genetics , nursing , organic chemistry , politics , political science , law , biology
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. © 1994 Wiley‐Liss, Inc.