| pubmed-article:12381853 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0035647 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0332161 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C1442792 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0036576 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0444504 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0681842 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0205360 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0441722 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C0678594 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C1561577 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C1514811 | lld:lifeskim |
| pubmed-article:12381853 | lifeskim:mentions | umls-concept:C1706462 | lld:lifeskim |
| pubmed-article:12381853 | pubmed:issue | 11 | lld:pubmed |
| pubmed-article:12381853 | pubmed:dateCreated | 2002-10-16 | lld:pubmed |
| pubmed-article:12381853 | pubmed:abstractText | The distance-dependent structure-derived potentials developed so far all employed a reference state that can be characterized as a residue (atom)-averaged state. Here, we establish a new reference state called the distance-scaled, finite ideal-gas reference (DFIRE) state. The reference state is used to construct a residue-specific all-atom potential of mean force from a database of 1011 nonhomologous (less than 30% homology) protein structures with resolution less than 2 A. The new all-atom potential recognizes more native proteins from 32 multiple decoy sets, and raises an average Z-score by 1.4 units more than two previously developed, residue-specific, all-atom knowledge-based potentials. When only backbone and C(beta) atoms are used in scoring, the performance of the DFIRE-based potential, although is worse than that of the all-atom version, is comparable to those of the previously developed potentials on the all-atom level. In addition, the DFIRE-based all-atom potential provides the most accurate prediction of the stabilities of 895 mutants among three knowledge-based all-atom potentials. Comparison with several physical-based potentials is made. | lld:pubmed |
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| pubmed-article:12381853 | pubmed:language | eng | lld:pubmed |
| pubmed-article:12381853 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:12381853 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:12381853 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:12381853 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:12381853 | pubmed:month | Nov | lld:pubmed |
| pubmed-article:12381853 | pubmed:issn | 0961-8368 | lld:pubmed |
| pubmed-article:12381853 | pubmed:author | pubmed-author:ZhouHongyiH | lld:pubmed |
| pubmed-article:12381853 | pubmed:author | pubmed-author:ZhouYaoqiY | lld:pubmed |
| pubmed-article:12381853 | pubmed:issnType | Print | lld:pubmed |
| pubmed-article:12381853 | pubmed:volume | 11 | lld:pubmed |
| pubmed-article:12381853 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:12381853 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:12381853 | pubmed:pagination | 2714-26 | lld:pubmed |
| pubmed-article:12381853 | pubmed:dateRevised | 2009-11-18 | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:meshHeading | pubmed-meshheading:12381853... | lld:pubmed |
| pubmed-article:12381853 | pubmed:year | 2002 | lld:pubmed |
| pubmed-article:12381853 | pubmed:articleTitle | Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. | lld:pubmed |
| pubmed-article:12381853 | pubmed:affiliation | Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA. | lld:pubmed |
| pubmed-article:12381853 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:12381853 | pubmed:publicationType | Research Support, Non-U.S. Gov't | lld:pubmed |
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