EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search.

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ID: 20315
2019
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Abstract
Protein-protein docking algorithms aim to predict the 3D structure of a binary complex using the structures of the individual proteins. This typically involves searching and scoring in a six-dimensional space. Many docking algorithms use FFT techniques to exhaustively cover the search space and to accelerate the scoring calculation. However, FFT docking results often depend on the initial protein orientations with respect to the Fourier sampling grid. Furthermore, Fourier-transforming a physics-base force field can involve a serious loss of precision.Here, we present EROS-DOCK, an algorithm to rigidly dock two proteins using a series of exhaustive 3D rotational searches in which non-clashing orientations are scored using the ATTRACT coarse-grained force field model. The rotational space is represented as a quaternion "π-ball", which is systematically sub-divided in a "branch-and-bound" manner, allowing efficient pruning of rotations that will give steric clashes. The algorithm was tested on 173 Docking Benchmark complexes, and results were compared with those of ATTRACT and ZDOCK. According to the CAPRI quality criteria, EROS-DOCK typically gives more acceptable or medium quality solutions than ATTRACT and ZDOCK.The EROS-DOCK program is available for download at http://erosdock.loria.fr.Supplementary data are available at Bioinformatics online.
Reference Key
ruiz2019erosdockbioinformatics Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Ruiz, Maria Elisa Echartea;de Beauchêne, Isaure Chauvot;Ritchie, David W;
Journal Bioinformatics
Year 2019
DOI
btz434
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