New measures for estimating surface complementarity and packing at protein-protein interfaces

FEBS Lett. 2010 Mar 19;584(6):1163-8. doi: 10.1016/j.febslet.2010.02.021. Epub 2010 Feb 12.

Abstract

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein-protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein-protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein-protein contacts, especially from large protein complexes and large-scale structural studies (http://pallab.serc.iisc.ernet.in/nip_nsc).

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Binding Sites
  • Crystallography, X-Ray
  • Dimerization
  • Efficiency
  • Models, Molecular
  • Protein Binding
  • Protein Conformation*
  • Protein Folding*
  • Protein Interaction Domains and Motifs / physiology
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry
  • Proteins / metabolism
  • Surface Properties

Substances

  • Proteins