11344256

Source:http://linkedlifedata.com/resource/pubmed/id/11344256

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0033684, umls-concept:C0678538, umls-concept:C0870781
pubmed:issue	11
pubmed:dateCreated	2001-5-24
pubmed:abstractText	The hierarchical properties of potential energy landscapes have been used to gain insight into thermodynamic and kinetic properties of protein ensembles. It also may be possible to use them to direct computational searches for thermodynamically stable macroscopic states, i.e., computational protein folding. To this end, we have developed a top-down search procedure in which conformation space is recursively dissected according to the intrinsic hierarchical structure of a landscape's effective-energy barriers. This procedure generates an inverted tree similar to the disconnectivity graphs generated by local minima-clustering methods, but it fundamentally differs in the manner in which the portion of the tree that is to be computationally explored is selected. A key ingredient is a branch-selection algorithm that takes advantage of statistically predictive properties of the landscape to guide searches down the tree branches that are most likely to lead to the physically relevant macroscopic states. Using the computational folding of a beta-hairpin-forming peptide as an example, we show that such predictive properties indeed exist and can be used for structure prediction by free-energy global minimization.
pubmed:commentsCorrections	http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-10639131, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-11226239, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-2748581, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-3478708, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-7618103, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-7886447, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-8430090, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-8539254, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-8673604, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-9032061, http://linkedlifedata.com/resource/pubmed/commentcorrection/11344256-9348663
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/7505876
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/Proteins
pubmed:status	MEDLINE
pubmed:month	May
pubmed:issn	0027-8424
pubmed:author	pubmed-author:ChurchB WBW, pubmed-author:ShallowayDD
pubmed:issnType	Print
pubmed:day	22
pubmed:volume	98
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	6098-103
pubmed:dateRevised	2010-9-14
pubmed:meshHeading	pubmed-meshheading:11344256-Algorithms, pubmed-meshheading:11344256-Energy Transfer, pubmed-meshheading:11344256-Probability, pubmed-meshheading:11344256-Protein Conformation, pubmed-meshheading:11344256-Proteins, pubmed-meshheading:11344256-Thermodynamics
pubmed:year	2001
pubmed:articleTitle	Top-down free-energy minimization on protein potential energy landscapes.
pubmed:affiliation	Biophysics Program, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't