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dc.contributor.authorYang, Yuedong
dc.contributor.authorZhou, Yaoqi
dc.date.accessioned2018-11-12T12:30:57Z
dc.date.available2018-11-12T12:30:57Z
dc.date.issued2008
dc.date.modified2014-03-31T23:44:27Z
dc.identifier.issn0961-8368
dc.identifier.doi10.1110/ps.033480.107
dc.identifier.urihttp://hdl.handle.net/10072/57584
dc.description.abstractOne of the common methods for assessing energy functions of proteins is selection of native or nearnative structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all-atom statistical energy functions, DFIRE (distance-scaled, finite, ideal-gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence-position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of shortrange interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 Aࠧlobal root-meansquared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherWiley-Blackwell Publishing, Inc.
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom1212
dc.relation.ispartofpageto1219
dc.relation.ispartofjournalProtein Science
dc.relation.ispartofvolume17
dc.rights.retentionY
dc.subject.fieldofresearchBiochemistry and cell biology
dc.subject.fieldofresearchTheory of computation
dc.subject.fieldofresearchOther information and computing sciences
dc.subject.fieldofresearchcode3101
dc.subject.fieldofresearchcode4613
dc.subject.fieldofresearchcode4699
dc.titleAb initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2008
gro.hasfulltextNo Full Text
gro.griffith.authorZhou, Yaoqi
gro.griffith.authorYang, Yuedong


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