Hydrophobic docking: A proposed enhancement to molecular recognition techniques

Ilya A. Vakser, Claude Aflalo

Research output: Contribution to journalArticlepeer-review

174 Scopus citations

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.

Original languageEnglish
Pages (from-to)320-329
Number of pages10
JournalProteins: Structure, Function, and Bioinformatics
Volume20
Issue number4
DOIs
StatePublished - 1 Jan 1994

Keywords

  • docking algorithm
  • hydrophobicity
  • macromolecular surface complementarity
  • protein recognition

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Fingerprint

Dive into the research topics of 'Hydrophobic docking: A proposed enhancement to molecular recognition techniques'. Together they form a unique fingerprint.

Cite this