A refined, efficient mean solvation force model that includes the interior volume contribution.

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dc.contributor.author Allison, Jane R
dc.contributor.author Boguslawski, Katharina
dc.contributor.author Fraternali, Franca
dc.contributor.author van Gunsteren, Wilfred F
dc.coverage.spatial United States
dc.date.accessioned 2022-05-24T21:57:41Z
dc.date.available 2022-05-24T21:57:41Z
dc.date.issued 2011-04
dc.identifier.citation (2011). The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter, 115(15), 4547-4557.
dc.identifier.issn 1520-6106
dc.identifier.uri https://hdl.handle.net/2292/59486
dc.description.abstract A refined implicit aqueous solvation model is proposed for the simulation of biomolecules without the explicit inclusion of the solvent degrees of freedom. The mean force due to solvation is approximated by the derivative of a simple analytic function of the solvent accessible surface area combined with two atomic solvation parameters, as described previously, with the addition of a novel term to account for the interaction of the interior atoms of the solute with the solvent. The extended model is parametrized by comparing the structural properties and energies computed from simulations of six test proteins of varying sizes and shapes using the new solvation energy term with the corresponding values obtained from simulations in vacuum, using the original implicit solvent model and in explicit water, and from the X-ray or NMR model structures. The mean solvation model proposed here improves the structural properties relative to vacuum simulations and relative to the simpler model that neglects the volume contribution, while remaining significantly more efficient than simulations in explicit water.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartofseries The journal of physical chemistry. B
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 Animals
dc.subject Humans
dc.subject Water
dc.subject Proteins
dc.subject Solvents
dc.subject Thermodynamics
dc.subject Models, Chemical
dc.subject Models, Molecular
dc.subject Computer Simulation
dc.subject Science & Technology
dc.subject Physical Sciences
dc.subject Chemistry, Physical
dc.subject Chemistry
dc.subject MOLECULAR-DYNAMICS SIMULATIONS
dc.subject SIMPLE COMPUTATIONAL MODEL
dc.subject ACCESSIBLE SURFACE-AREA
dc.subject IMPLICIT SOLVENT MODEL
dc.subject FREE-ENERGIES
dc.subject SOLUTE MOLECULES
dc.subject HYDRATION
dc.subject DISPERSION
dc.subject MECHANICS
dc.subject 0306 Physical Chemistry (incl. Structural)
dc.subject 02 Physical Sciences
dc.subject 03 Chemical Sciences
dc.subject 09 Engineering
dc.title A refined, efficient mean solvation force model that includes the interior volume contribution.
dc.type Journal Article
dc.identifier.doi 10.1021/jp2017117
pubs.issue 15
pubs.begin-page 4547
pubs.volume 115
dc.date.updated 2022-04-28T03:31:14Z
dc.rights.holder Copyright: The author en
dc.identifier.pmid 21434626 (pubmed)
pubs.author-url https://www.ncbi.nlm.nih.gov/pubmed/21434626
pubs.end-page 4557
pubs.publication-status Published
dc.rights.accessrights http://purl.org/eprint/accessRights/RetrictedAccess en
pubs.subtype Research Support, Non-U.S. Gov't
pubs.subtype Journal Article
pubs.elements-id 739605
pubs.org-id Science
pubs.org-id Biological Sciences
dc.identifier.eissn 1520-5207
pubs.record-created-at-source-date 2022-04-28
pubs.online-publication-date 2011-03-24


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