Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

Bioinformatics. 2015 Mar 1;31(5):707-13. doi: 10.1093/bioinformatics/btu724. Epub 2014 Oct 29.


Motivation: Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects.

Results: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods.

Availability and implementation: CONTACT:

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Binding Sites
  • Computer Simulation
  • Humans
  • Ligands
  • Mathematical Computing*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*


  • Ligands
  • Proteins