title: 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.
  
  
  
  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.
authors.affiliation: Department of Biomedical Engineering.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Department of Biomedical Engineering Department of Chemistry, Boston University, Boston, MA 02215, USA.
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.affiliation: Department of Applied Mathematics and Statistics Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D000818:Animals; D005583:Fourier Analysis; D006801:Humans; D062105:Molecular Docking Simulation; D011506:Proteins; D012984:Software
chemical_list: D011506:Proteins