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

Maria Ruiz­ Echartea 1 Isaure Chauvot de Beauchêne 1 David Ritchie 1
1 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
Abstract : Motivation: 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. Results: 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 subdivided 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 typcially gives more acceptable or medium quality solutions than ATTRACT and ZDOCK. Availability: The EROS-DOCK program is available for download at http://erosdock.loria.fr.
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Maria Ruiz­ Echartea, Isaure Chauvot de Beauchêne, David Ritchie. EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search. Bioinformatics, Oxford University Press (OUP), 2019, 35 (23), pp.5003-5010. ⟨10.1093/bioinformatics/btz434⟩. ⟨hal-02269812⟩

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