10336385

Source:http://linkedlifedata.com/resource/pubmed/id/10336385

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0033684, umls-concept:C0184511, umls-concept:C0205195, umls-concept:C0524637, umls-concept:C1510464, umls-concept:C2348519
pubmed:issue	1
pubmed:dateCreated	1999-5-18
pubmed:abstractText	We describe the development of a scoring function based on the decomposition P(structure/sequence) proportional to P(sequence/structure) *P(structure), which outperforms previous scoring functions in correctly identifying native-like protein structures in large ensembles of compact decoys. The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the assembly of beta-strands into beta-sheets. The efficacies of a wide variety of sequence-dependent and sequence-independent features of protein structures for recognizing native-like structures were systematically evaluated using ensembles of approximately 30,000 compact conformations with fixed secondary structure for each of 17 small protein domains. The best results were obtained using a core scoring function with P(sequence/structure) parameterized similarly to our previous work (Simons et al., J Mol Biol 1997;268:209-225] and P(structure) focused on secondary structure packing preferences; while several additional features had some discriminatory power on their own, they did not provide any additional discriminatory power when combined with the core scoring function. Our results, on both the training set and the independent decoy set of Park and Levitt (J Mol Biol 1996;258:367-392), suggest that this scoring function should contribute to the prediction of tertiary structure from knowledge of sequence and secondary structure.
pubmed:grant	http://linkedlifedata.com/resource/pubmed/grant/T32 GM07270
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/8700181
pubmed:citationSubset	IM
pubmed:status	MEDLINE
pubmed:month	Jan
pubmed:issn	0887-3585
pubmed:author	pubmed-author:BakerDD, pubmed-author:BystroffCC, pubmed-author:FoxB ABA, pubmed-author:KooperbergCC, pubmed-author:RuczinskiII, pubmed-author:SimonsK TKT
pubmed:issnType	Print
pubmed:day	1
pubmed:volume	34
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	82-95
pubmed:dateRevised	2007-11-14
pubmed:meshHeading	pubmed-meshheading:10336385-Models, Statistical, pubmed-meshheading:10336385-Protein Conformation, pubmed-meshheading:10336385-Protein Structure, Secondary, pubmed-meshheading:10336385-Protein Structure, Tertiary
pubmed:year	1999
pubmed:articleTitle	Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.
pubmed:affiliation	Department of Biochemistry, University of Washington, Seattle 98195, USA.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't