Linked Life Data

11478870

Source:http://linkedlifedata.com/resource/pubmed/id/11478870

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2001-7-31
pubmed:abstractText
Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in extending the limits of side-chain prediction for core residues to about 0.7 A rmsd from native, and 94 % and 89 % of chi(1) and chi(1+2 ) dihedral angles correctly predicted to within 20 degrees of native, respectively. These results are obtained using a force-field that accounts for only van der Waals interactions and torsional potentials. Prediction accuracy is strongly dependent on the rotamer library used. That is, a complete and detailed rotamer library is essential. The greatest accuracy was obtained with an extensive rotamer library, containing over 7560 members, in which bond lengths and bond angles were taken from the database rather than simply assuming idealized values. Perhaps the most surprising finding is that the combinatorial problem normally associated with the prediction of the side-chain conformation does not appear to be important. This conclusion is based on the fact that the prediction of the conformation of a single side-chain with all others fixed in their native conformations is only slightly more accurate than the simultaneous prediction of all side-chain dihedral angles.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0022-2836
pubmed:author
pubmed:copyrightInfo
Copyright 2001 Academic Press.
pubmed:issnType
Print
pubmed:day
10
pubmed:volume
311
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
421-30
pubmed:dateRevised
2007-11-15
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Extending the accuracy limits of prediction for side-chain conformations.
pubmed:affiliation
Department of Biochemistry and Molecular Biophysics BB221, Columbia University, New York, NY 10032, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.