Linked Life Data

11928507

Source:http://linkedlifedata.com/resource/pubmed/id/11928507

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2002-4-3
pubmed:abstractText
A new method for considering solvation when calculating electrostatics for protein docking is proposed. The solvent-exposed charges are attenuated by induced solvent polarization charges. Modified charges are pre-calculated and the correction doesn't affect the speed of the actual simulation. The new Screened Charge Electrostatic Model (SChEM) results in an improved discrimination of near-native solutions from false positives in docking simulations as compared to conventional 'non-solvated' charge assignment. A series of protein-protein complexes were analyzed by running automated rigid-body Monte-Carlo docking simulations using the 3-D coordinates of the unbound components. In all but one case, the use of solvation screened charges for electrostatic calculations helped to improve the rank of the near-native solution after rigid-body simulations. The SChEM also drastically improved the results of the subsequent refinement of the interface side-chains. In all cases the final lowest energy solution was found within 3.0 A r.m.s.d. of the crystal structure.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1793-5091
pubmed:author
pubmed:issnType
Print
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
552-63
pubmed:dateRevised
2008-11-21
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Screened charge electrostatic model in protein-protein docking simulations.
pubmed:affiliation
Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jfrecio@scripps.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.