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Journal Articles Proteins: Structure, Function, and Genetics Year : 2000

Protein docking using spherical polar Fourier correlations

Graham J.L. Kemp
  • Function : Author

Abstract

We present a new computational method of docking pairs of proteins by using spherical polar Fourier correlations to accelerate the search for candidate low-energy conformations. Interaction energies are estimated using a hydrophobic excluded volume model derived from the notion of overlapping surface skins, augmented by a rigorous but soft model of electrostatic complementarity. This approach has several advantages over former three-dimensional grid-based fast Fourier transform (FFT) docking correlation methods even though there is no analogue to the FFT in a spherical polar representation. For example, a complete search over all six rigid-body degrees of freedom can be performed by rotating and translating only the initial expansion coefficients, many infeasible orientations may be eliminated rapidly using only low-resolution terms, and the correlations are easily localized around known binding epitopes when this knowledge is available. Typical execution times on a single processor workstation range from 2 hours for a global search (5 × 10^8 trial orientations) to a few minutes for a local search (over 6 × 10^7 orientations). The method is illustrated with several domain dimer and enzyme-inhibitor complexes and 20 large antibody-antigen complexes, using both the bound and (when available) unbound subunits. The correct conformation of the complex is frequently identified when docking bound subunits, and a good docking orientation is ranked within the top 20 in 11 out of 18 cases when starting from unbound subunits.

Dates and versions

inria-00434273 , version 1 (21-11-2009)

Identifiers

Cite

David Ritchie, Graham J.L. Kemp. Protein docking using spherical polar Fourier correlations. Proteins: Structure, Function, and Genetics, 2000, 39, pp.178-194. ⟨10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6⟩. ⟨inria-00434273⟩
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