EROS-DOCK: protein–protein docking using exhaustive branch-and-bound rotational search

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 6D 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 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. Availability and implementation The EROS-DOCK program is available for download at http://erosdock.loria.fr. Supplementary information Supplementary data are available at Bioinformatics online.

Protein–Protein Docking: Past, Present, and Future

“…Results show that the minimum energy structure obtained by docking proteins in reduced representation resembles with experimental structure. This scheme is effectively used in many docking techniques [8][9][10].…”

Information-driven modeling of biomolecular complexes

“…The Exhaustive Rotational Search based Docking (EROS-DOCK) [33] is another docking software that uses information to avoid sampling the subspace that does not satisfy a given restraint. It also belongs to the very exclusive group of docking software that can handle both restraints and multi-body docking (i.e., the modeling of complexes consisting of more than two components), together with the pioneer HADDOCK and ATTRACT [25,34].…”

Using restraints in EROS‐DOCK improves model quality in pairwise and multicomponent protein docking

“…In typical cases, when using this approach, around 95% of the search space may be eliminated from consideration. In other words, ATTRACT CG bead interactions need only be calculated for about 5% of the rotational search space [12].…”