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Prots: A fragment based protein thermo‐stability potential

dc.contributor.authorLi, Yunqien_US
dc.contributor.authorZhang, Jianen_US
dc.contributor.authorTai, Daviden_US
dc.contributor.authorRussell Middaugh, C.en_US
dc.contributor.authorZhang, Yangen_US
dc.contributor.authorFang, Jianwenen_US
dc.date.accessioned2012-01-05T22:06:33Z
dc.date.available2013-03-04T15:29:55Zen_US
dc.date.issued2012-01en_US
dc.identifier.citationLi, Yunqi; Zhang, Jian; Tai, David; Russell Middaugh, C.; Zhang, Yang; Fang, Jianwen (2012). "Prots: A fragment based protein thermo‐stability potential." Proteins: Structure, Function, and Bioinformatics 80(1): 81-92. <http://hdl.handle.net/2027.42/89526>en_US
dc.identifier.issn0887-3585en_US
dc.identifier.issn1097-0134en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/89526
dc.description.abstractDesigning proteins with enhanced thermo‐stability has been a main focus of protein engineering because of its theoretical and practical significance. Despite extensive studies in the past years, a general strategy for stabilizing proteins still remains elusive. Thus effective and robust computational algorithms for designing thermo‐stable proteins are in critical demand. Here we report PROTS, a sequential and structural four‐residue fragment based protein thermo‐stability potential. PROTS is derived from a nonredundant representative collection of thousands of thermophilic and mesophilic protein structures and a large set of point mutations with experimentally determined changes of melting temperatures. To the best of our knowledge, PROTS is the first protein stability predictor based on integrated analysis and mining of these two types of data. Besides conventional cross validation and blind testing, we introduce hypothetical reverse mutations as a means of testing the robustness of protein thermo‐stability predictors. In all tests, PROTS demonstrates the ability to reliably predict mutation induced thermo‐stability changes as well as classify thermophilic and mesophilic proteins. In addition, this white‐box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level. Proteins 2012; © 2011 Wiley Periodicals, Inc.en_US
dc.publisherWiley Subscription Services, Inc., A Wiley Companyen_US
dc.subject.otherProtein Stabilityen_US
dc.subject.otherThermophilicen_US
dc.subject.otherPredictionen_US
dc.subject.otherDataminingen_US
dc.subject.otherThermostability Potentialen_US
dc.titleProts: A fragment based protein thermo‐stability potentialen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelBiological Chemistryen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.contributor.affiliationumCenter for Computational Medicine and Bioinformatics, the University of Michigan Medical School, Ann Arbor, Michigan 48109en_US
dc.contributor.affiliationotherApplied Bioinformatics Laboratory, the University of Kansas, Lawrence, Kansas 66047en_US
dc.contributor.affiliationotherDepartment of Pharmaceutical Chemistry, the University of Kansas, Lawrence, Kansas 66047en_US
dc.contributor.affiliationotherApplied Bioinformatics Laboratory, the University of Kansas, 2034 Becker Dr., Lawrence, KS 66047en_US
dc.identifier.pmid21976375en_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/89526/1/23163_ftp.pdf
dc.identifier.doi10.1002/prot.23163en_US
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dc.owningcollnameInterdisciplinary and Peer-Reviewed


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