title: Exploring angular distance in protein-protein docking algorithms.
abstract: We present a two-stage hybrid-resolution approach for rigid-body protein-protein docking. The first stage is carried out at low-resolution (15°) angular sampling. In the second stage, we sample promising regions from the first stage at a higher resolution of 6°. The hybrid-resolution approach produces the same results as a 6° uniform sampling docking run, but uses only 17% of the computational time. We also show that the angular distance can be used successfully in clustering and pruning algorithms, as well as the characterization of energy funnels. Traditionally the root-mean-square-distance is used in these algorithms, but the evaluation is computationally expensive as it depends on both the rotational and translational parameters of the docking solutions. In contrast, the angular distances only depend on the rotational parameters, which are generally fixed for all docking runs. Hence the angular distances can be pre-computed, and do not add computational time to the post-processing of rigid-body docking results.
authors: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors: Thom
authors: T
authors: Vreven
authors: Howook
authors: H
authors: Hwang
authors: Zhiping
authors: Z
authors: Weng
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins