InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information

Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9. doi: 10.1093/nar/gkw340. Epub 2016 Apr 29.

Abstract

The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.

MeSH terms

  • Benchmarking
  • Evolution, Molecular*
  • Internet*
  • Molecular Docking Simulation*
  • Protein Interaction Maps*
  • Proteins / chemistry*
  • Sequence Alignment
  • Software*
  • User-Computer Interface

Substances

  • Proteins