Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses

Guillaume Launay; Masahito Ohue; Julia Prieto Santero; Yuri Matsuzaki; Cécile Hilpert; Nobuyuki Uchikoga; Takanori Hayashi; Juliette Martin

doi:10.3389/fmolb.2020.559005

Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses

Front Mol Biosci. 2020 Oct 21:7:559005. doi: 10.3389/fmolb.2020.559005. eCollection 2020.

Authors

Guillaume Launay¹, Masahito Ohue², Julia Prieto Santero¹, Yuri Matsuzaki³, Cécile Hilpert¹, Nobuyuki Uchikoga⁴, Takanori Hayashi², Juliette Martin¹

Affiliations

¹ CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, University of Lyon, Lyon, France.
² Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan.
³ Tokyo Tech Academy for Leadership, Tokyo Institute of Technology, Tokyo, Japan.
⁴ Department of Network Design, School of Interdisciplinary Mathematical Sciences, Meiji University, Tokyo, Japan.

Abstract

Scoring is a challenging step in protein-protein docking, where typically thousands of solutions are generated. In this study, we ought to investigate the contribution of consensus-rescoring, as introduced by Oliva et al. (2013) with the CONSRANK method, where the set of solutions is used to build statistics in order to identify recurrent solutions. We explore several ways to perform consensus-based rescoring on the ZDOCK decoy set for Benchmark 4. We show that the information of the interface size is critical for successful rescoring in this context, but that consensus rescoring in itself performs less well than traditional physics-based evaluation. The results of physics-based and consensus-based rescoring are partially overlapping, supporting the use of a combination of these approaches.

Keywords: docking; interface; prediction; protein–protein interaction; scoring.