Accounting for pairwise distance restraints in FFT-based protein-protein docking

Abstract

ClusPro is a heavily used protein-protein docking server based on the fast Fourier transform (FFT) correlation approach. While FFT enables global docking, accounting for pairwise distance restraints using penalty terms in the scoring function is computationally expensive. We use a different approach and directly select low energy solutions that also satisfy the given restraints. As expected, accounting for restraints generally improves the rank of near native predictions, while retaining or even improving the numerical efficiency of FFT based docking.

Availability and implementation: The software is freely available as part of the ClusPro web-based server at http://cluspro.org/nousername.php CONTACT: midas@laufercenter.org or vajda@bu.eduSupplementary information: Supplementary data are available at Bioinformatics online.