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Efficient generalized Born models for Monte Carlo simulations

Efficient generalized Born models for Monte Carlo simulations
Efficient generalized Born models for Monte Carlo simulations
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.
implicit solvent model, molecular-dynamics, solvation energies, parameterization, approximation, validation, inhibitors, surfaces, docking, hairpin
1549-9618
732-739
Michel, Julien
3dfda20a-a6fa-4214-8c7d-578f550b9ad7
Taylor, Richard D.
141004d4-95a6-44f1-93ce-ca36c1b34d61
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Michel, Julien
3dfda20a-a6fa-4214-8c7d-578f550b9ad7
Taylor, Richard D.
141004d4-95a6-44f1-93ce-ca36c1b34d61
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Michel, Julien, Taylor, Richard D. and Essex, Jonathan W. (2006) Efficient generalized Born models for Monte Carlo simulations. Journal of Chemical Theory and Computation, 2 (3), 732-739. (doi:10.1021/ct600069r).

Record type: Article

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.

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More information

Published date: 2006
Keywords: implicit solvent model, molecular-dynamics, solvation energies, parameterization, approximation, validation, inhibitors, surfaces, docking, hairpin

Identifiers

Local EPrints ID: 44498
URI: http://eprints.soton.ac.uk/id/eprint/44498
ISSN: 1549-9618
PURE UUID: 328937af-5e16-4555-9419-92bb0dabdfde
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 02 Mar 2007
Last modified: 03 Dec 2019 02:02

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