Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
5
pubmed:dateCreated
2001-3-6
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.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-10051588, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-10318909, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-10526364, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-11005847, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-1167625, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-1329944, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-1390743, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-1839175, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-3219397, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-3709525, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-4124164, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-4437206, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-4855768, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-7504550, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8229093, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8229096, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8515448, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8566533, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8672720, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-8757807, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9204280, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9311930, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9565758, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9657719, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9664845, http://linkedlifedata.com/resource/pubmed/commentcorrection/11226239-9769221
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
0027-8424
pubmed:author
pubmed:issnType
Print
pubmed:day
27
pubmed:volume
98
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
2329-33
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Recent improvements in prediction of protein structure by global optimization of a potential energy function.
pubmed:affiliation
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, 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