CavVis-A Field-of-View Geometric Algorithm for Protein Cavity Detection

J Chem Inf Model. 2019 Feb 25;59(2):786-796. doi: 10.1021/acs.jcim.8b00572. Epub 2019 Jan 25.

Abstract

Several geometric-based methods have been developed for the last two to three decades to detect and identify cavities (i.e., putative binding sites) on proteins, as needed to study protein-ligand interactions and protein docking. This paper introduces a new protein cavity method, called CavVis, which combines voxelization (i.e., a grid of voxels) and an analytic formulation of Gaussian surfaces that approximates the solvent-excluded surface. This method builds upon visibility of points on protein surface to find its cavities. Specifically, the visibility criterion combines three concepts we borrow from computer graphics, the field-of-view of each surface point, voxel ray casting, and back-face culling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Ligands
  • Models, Molecular*
  • Normal Distribution
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Surface Properties

Substances

  • Ligands
  • Proteins