Identification and visualization of protein binding regions with the ArDock server

Nucleic Acids Res. 2018 Jul 2;46(W1):W417-W422. doi: 10.1093/nar/gky472.

Abstract

ArDock (ardock.ibcp.fr) is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. ArDock ranks the surface residues of a protein according to their tendency to form interfaces in a set of predefined docking experiments between the query protein and a set of arbitrary protein probes. The ArDock methodology is derived from large scale cross-docking studies where it was observed that randomly chosen proteins tend to dock in a non-random way at protein surfaces. The method predicts interaction site of the protein, or alternate interfaces in the case of proteins with multiple interaction modes. The server takes a protein structure as input and computes a score for each surface residue. Its output focuses on the interactive visualization of results and on interoperability with other services.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Benchmarking
  • Binding Sites
  • Computational Biology / methods*
  • Databases, Protein
  • Humans
  • Internet
  • Ligands
  • Molecular Docking Simulation / methods*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Software*
  • Structural Homology, Protein*

Substances

  • Ligands
  • Proteins