| pubmed-article:11226239 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C1510464 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C0542341 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C0681842 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C0678538 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C2698650 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C2348867 | lld:lifeskim |
| pubmed-article:11226239 | lifeskim:mentions | umls-concept:C0332185 | lld:lifeskim |
| pubmed-article:11226239 | pubmed:issue | 5 | lld:pubmed |
| pubmed-article:11226239 | pubmed:dateCreated | 2001-3-6 | lld:pubmed |
| pubmed-article:11226239 | pubmed:abstractText | Recent improvements of a hierarchical ab initio or de novo approach for predicting both alpha and beta structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic alpha-helical protein of 70 residues was predicted to within 4.3 A alpha-carbon (C(alpha)) rms deviation (rmsd) whereas, for other alpha-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 A C(alpha) rmsd. Whereas beta structures can now be predicted with the new procedure, the success rate for alpha/beta- and beta-proteins is lower than that for alpha-proteins at present. For the beta portions of alpha/beta structures, the C(alpha) rmsd's are less than 6.0 A for contiguous fragments of 30-40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a C(alpha) rmsd less than 6.0 A. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence. | lld:pubmed |
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| pubmed-article:11226239 | pubmed:language | eng | lld:pubmed |
| pubmed-article:11226239 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:11226239 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:11226239 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:11226239 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:11226239 | pubmed:month | Feb | lld:pubmed |
| pubmed-article:11226239 | pubmed:issn | 0027-8424 | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:ScheragaH AHA | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:LeeJJ | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:SaundersJJ | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:GibsonK DKD | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:YuY ZYZ | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:RipollD RDR | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:LiwoAA | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:OldziejSS | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:CzaplewskaKK | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:Ka?mierkiewic... | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:WedemeyerW... | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:PillardyJJ | lld:pubmed |
| pubmed-article:11226239 | pubmed:author | pubmed-author:ArnautovaY... | lld:pubmed |
| pubmed-article:11226239 | pubmed:issnType | Print | lld:pubmed |
| pubmed-article:11226239 | pubmed:day | 27 | lld:pubmed |
| pubmed-article:11226239 | pubmed:volume | 98 | lld:pubmed |
| pubmed-article:11226239 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:11226239 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:11226239 | pubmed:pagination | 2329-33 | lld:pubmed |
| pubmed-article:11226239 | pubmed:dateRevised | 2009-11-18 | lld:pubmed |
| pubmed-article:11226239 | pubmed:meshHeading | pubmed-meshheading:11226239... | lld:pubmed |
| pubmed-article:11226239 | pubmed:meshHeading | pubmed-meshheading:11226239... | lld:pubmed |
| pubmed-article:11226239 | pubmed:meshHeading | pubmed-meshheading:11226239... | lld:pubmed |
| pubmed-article:11226239 | pubmed:year | 2001 | lld:pubmed |
| pubmed-article:11226239 | pubmed:articleTitle | Recent improvements in prediction of protein structure by global optimization of a potential energy function. | lld:pubmed |
| pubmed-article:11226239 | pubmed:affiliation | Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA. | lld:pubmed |
| pubmed-article:11226239 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:11226239 | pubmed:publicationType | Research Support, U.S. Gov't, P.H.S. | lld:pubmed |
| pubmed-article:11226239 | pubmed:publicationType | Research Support, U.S. Gov't, Non-P.H.S. | lld:pubmed |
| pubmed-article:11226239 | pubmed:publicationType | Research Support, Non-U.S. Gov't | lld:pubmed |
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