SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses

J Chem Inf Model. 2017 Feb 27;57(2):127-132. doi: 10.1021/acs.jcim.6b00513. Epub 2017 Jan 17.

Abstract

We have recently introduced the "SQM/COSMO" scoring function which combines a semiempirical quantum mechanical description of noncovalent interactions at the PM6-D3H4X level and the COSMO implicit model of solvation. This approach outperformed standard scoring functions but faced challenges with a metalloprotein featuring a Zn2+···S- interaction. Here, we invoke SCC-DFTB3-D3H4, a higher-level SQM method, and observe improved behavior for the metalloprotein and high-quality results for the other systems. This method holds promise for diverse protein-ligand complexes including metalloproteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Letter

MeSH terms

  • Ligands
  • Metalloproteins / metabolism*
  • Protein Binding
  • Quantum Theory*
  • Thermodynamics

Substances

  • Ligands
  • Metalloproteins