Switch to
| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
2
|
| pubmed:dateCreated |
1996-6-24
|
| pubmed:abstractText |
This study generates ensembles of decoy or test structures for eight small proteins with a variety of different folds. Between 35,000 and 200,000 decoys were generated for each protein using our four-state off-lattice model together with a novel relaxation method. These give compact self-avoiding conformations each constrained to have native secondary structure. Ensembles of these decoy conformations were used to test the ability of several types of empirical contact, surface area and distance-dependent energy functions to distinguish between correct and incorrect conformations. These tests have shown that none of the functions is able to distinguish consistently either the X-ray conformation or the near-native conformations from others which are incorrect. Certain combinations of two of these energy functions were able, however, consistently to identify X-ray structures from amongst the decoy conformations. These same combinations are better also at identifying near-native conformations, consistently finding them with a hundred-fold higher frequency than chance. The fact that these combination energy functions perform better than generally accepted energy functions suggests their future use in folding simulations and perhaps threading predictions.
|
| pubmed:grant | |
| pubmed:language |
eng
|
| pubmed:journal | |
| pubmed:citationSubset |
IM
|
| pubmed:chemical | |
| pubmed:status |
MEDLINE
|
| pubmed:month |
May
|
| pubmed:issn |
0022-2836
|
| pubmed:author | |
| pubmed:issnType |
Print
|
| pubmed:day |
3
|
| pubmed:volume |
258
|
| pubmed:owner |
NLM
|
| pubmed:authorsComplete |
Y
|
| pubmed:pagination |
367-92
|
| pubmed:dateRevised |
2007-11-14
|
| pubmed:meshHeading | |
| pubmed:year |
1996
|
| pubmed:articleTitle |
Energy functions that discriminate X-ray and near native folds from well-constructed decoys.
|
| pubmed:affiliation |
Department of Structural Biology, Stanford School of Medicine, CA 94305, USA.
|
| pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.,
Research Support, U.S. Gov't, Non-P.H.S.
|