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Article: Improved amino acid flexibility parameters

TitleImproved amino acid flexibility parameters
Authors
KeywordsB-factor
Atomic displacement parameter
Gumbel distribution
Extreme value distribution
Flexibility
Issue Date2003
PublisherCold Spring Harbor Laboratory Press, Publications Department. The Journal's web site is located at http://www.proteinscience.org/
Citation
Protein Science, 2003, v. 12 n. 5, p. 1060-1072 How to Cite?
AbstractProtein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.
Persistent Identifierhttp://hdl.handle.net/10722/48981
ISSN
2015 Impact Factor: 3.039
2015 SCImago Journal Rankings: 2.029
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorSmith, DKen_HK
dc.contributor.authorRadivojac, Pen_HK
dc.contributor.authorObradovic, Zen_HK
dc.contributor.authorDunker, AKen_HK
dc.contributor.authorZhu, Gen_HK
dc.date.accessioned2008-06-12T06:31:18Z-
dc.date.available2008-06-12T06:31:18Z-
dc.date.issued2003en_HK
dc.identifier.citationProtein Science, 2003, v. 12 n. 5, p. 1060-1072en_HK
dc.identifier.issn0961-8368en_HK
dc.identifier.urihttp://hdl.handle.net/10722/48981-
dc.description.abstractProtein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.en_HK
dc.format.extent388 bytes-
dc.format.mimetypetext/html-
dc.languageengen_HK
dc.publisherCold Spring Harbor Laboratory Press, Publications Department. The Journal's web site is located at http://www.proteinscience.org/en_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectB-factoren_HK
dc.subjectAtomic displacement parameteren_HK
dc.subjectGumbel distributionen_HK
dc.subjectExtreme value distributionen_HK
dc.subjectFlexibilityen_HK
dc.titleImproved amino acid flexibility parametersen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0961-8368&volume=12&issue=5&spage=1060&epage=1072&date=2003&atitle=Improved+amino+acid+flexibility+parametersen_HK
dc.identifier.emailSmith, DK: dsmith@hkucc.hku.hken_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1110/ps.0236203en_HK
dc.identifier.pmid12717028-
dc.identifier.pmcidPMC2323876en_HK
dc.identifier.scopuseid_2-s2.0-0037407015-
dc.identifier.hkuros83988-
dc.identifier.isiWOS:000182486800017-
dc.identifier.citeulike456023-

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