Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.

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dc.contributor.author Kleinjung, Jens
dc.contributor.author Scott, Walter RP
dc.contributor.author Allison, Jane R
dc.contributor.author van Gunsteren, Wilfred F
dc.contributor.author Fraternali, Franca
dc.coverage.spatial United States
dc.date.accessioned 2022-05-24T23:04:52Z
dc.date.available 2022-05-24T23:04:52Z
dc.date.issued 2012-07
dc.identifier.citation (2012). Journal of Chemical Theory and Computation, 8(7), 2391-2403.
dc.identifier.issn 1549-9618
dc.identifier.uri https://hdl.handle.net/2292/59492
dc.description.abstract Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent-solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom-specific solvation parameter σ(i) (SASA). A procedure for the determination of values for the σ(i) (SASA) parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σ(i) (SASA) parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σ(g) (SASA) was obtained via partitioning of the atom-type σ(i) (SASA) distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartofseries Journal of chemical theory and computation
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm
dc.subject Science & Technology
dc.subject Physical Sciences
dc.subject Chemistry, Physical
dc.subject Physics, Atomic, Molecular & Chemical
dc.subject Chemistry
dc.subject Physics
dc.subject PROTEIN STRUCTURES
dc.subject GENERALIZED BORN
dc.subject CONFORMATIONAL SPACE
dc.subject SOLVENT MODELS
dc.subject LEAP-DYNAMICS
dc.subject FREE-ENERGIES
dc.subject SURFACES
dc.subject 0306 Physical Chemistry (incl. Structural)
dc.subject 0307 Theoretical and Computational Chemistry
dc.subject 0601 Biochemistry and Cell Biology
dc.subject 0803 Computer Software
dc.title Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.
dc.type Journal Article
dc.identifier.doi 10.1021/ct200390j
pubs.issue 7
pubs.begin-page 2391
pubs.volume 8
dc.date.updated 2022-04-28T03:29:37Z
dc.rights.holder Copyright: The author en
dc.identifier.pmid 23180979 (pubmed)
pubs.author-url https://www.ncbi.nlm.nih.gov/pubmed/23180979
pubs.end-page 2403
pubs.publication-status Published
dc.rights.accessrights http://purl.org/eprint/accessRights/RetrictedAccess en
pubs.subtype research-article
pubs.subtype Journal Article
pubs.elements-id 739593
pubs.org-id Science
pubs.org-id Biological Sciences
dc.identifier.eissn 1549-9626
pubs.record-created-at-source-date 2022-04-28
pubs.online-publication-date 2012-06-26


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