Linked Life Data

10048329

Source:http://linkedlifedata.com/resource/pubmed/id/10048329

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
1999-5-6
pubmed:abstractText
We examine the similarities and differences between two widely used knowledge-based potentials, which are expressed as contact matrices (consisting of 210 elements) that gives a scale for interaction energies between the naturally occurring amino acid residues. These are the Miyazawa-Jernigan contact interaction matrix M and the potential matrix S derived by Skolnick J et al., 1997, Protein Sci 6:676-688. Although the correlation between the two matrices is good, there is a relatively large dispersion between the elements. We show that when Thr is chosen as a reference solvent within the Miyazawa and Jernigan scheme, the dispersion between the M and S matrices is reduced. The resulting interaction matrix B gives hydrophobicities that are in very good agreement with experiment. The small dispersion between the S and B matrices, which arises due to differing reference states, is shown to have dramatic effect on the predicted native states of lattice models of proteins. These findings and other arguments are used to suggest that for reliable predictions of protein structures, pairwise additive potentials are not sufficient. We also establish that optimized protein sequences can tolerate relatively large random errors in the pair potentials. We conjecture that three body interaction may be needed to predict the folds of proteins in a reliable manner.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-1004017, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-2385597, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-3398047, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-5555568, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-7648326, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8327519, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8495198, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8535247, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8592696, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8604144, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8609636, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8728652, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-8740358, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-9000638, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-9070450, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-9094335, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-9514266, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-9562550, http://linkedlifedata.com/resource/pubmed/commentcorrection/10048329-957439
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
0961-8368
pubmed:author
pubmed:issnType
Print
pubmed:volume
8
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
361-9
pubmed:dateRevised
2010-9-13
pubmed:meshHeading
pubmed:year
1999
pubmed:articleTitle
Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes.
pubmed:affiliation
Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, Non-P.H.S.