Efficient Generalized Born Models for Monte Carlo Simulations

Julien Michel; Richard D Taylor; Jonathan W Essex

doi:10.1021/ct600069r

Efficient Generalized Born Models for Monte Carlo Simulations

J Chem Theory Comput. 2006 May;2(3):732-9. doi: 10.1021/ct600069r.

Authors

Julien Michel¹, Richard D Taylor¹, Jonathan W Essex¹

Affiliation

¹ School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Cambridge CB4 0QA, U.K.

PMID: 26626678
DOI: 10.1021/ct600069r

Abstract

The Generalized Born Surface Area theory (GBSA) has become a popular method to model the solvation of biomolecules. While efficient in the context of molecular dynamics simulations, GBSA calculations do not integrate well with Monte Carlo simulations because of the nonlocal nature of the Generalized Born energy. We present a method by which Monte Carlo Generalized Born simulations can be made seven to eight times faster on a protein-ligand binding free energy calculation with little or no loss of accuracy. The method can be employed in any type of Monte Carlo or Hybrid Monte Carlo-molecular dynamics simulation and should prove useful in numerous applications.