Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors

J Chem Inf Model. 2020 Mar 23;60(3):1390-1398. doi: 10.1021/acs.jcim.9b01066. Epub 2020 Feb 25.

Abstract

In this work, we describe the application of the Zernike formalism to quantitatively characterize the binding pockets of two sets of biologically relevant systems. Such an approach, when applied to molecular dynamics trajectories, is able to pinpoint the subtle differences between very similar molecular regions and their impact on the local propensity to ligand binding, allowing us to quantify such differences. The statistical robustness of our procedure suggests that it is very suitable to describe protein binding sites and protein-ligand interactions within a rigorous and well-defined framework.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Ligands
  • Protein Binding
  • Protein Conformation
  • Proteins* / metabolism

Substances

  • Ligands
  • Proteins