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dc.contributor.authorZhao, Huiying
dc.contributor.authorYang, Yuedong
dc.contributor.authorvon Itzstein, Mark
dc.contributor.authorZhou, Yaoqi
dc.date.accessioned2017-05-03T15:57:43Z
dc.date.available2017-05-03T15:57:43Z
dc.date.issued2014
dc.identifier.issn0192-8651
dc.identifier.doi10.1002/jcc.23730
dc.identifier.urihttp://hdl.handle.net/10072/65546
dc.description.abstractCarbohydrate-binding proteins (CBPs) are potential biomarkers and drug targets. However, the interactions between carbohydrates and proteins are challenging to study experimentally and computationally because of their low binding affinity, high flexibility, and the lack of a linear sequence in carbohydrates as exists in RNA, DNA, and proteins. Here, we describe a structure-based function-prediction technique called SPOT-Struc that identifies carbohydrate-recognizing proteins and their binding amino acid residues by structural alignment program SPalign and binding affinity scoring according to a knowledge-based statistical potential based on the distance-scaled finite-ideal gas reference state (DFIRE). The leave-one-out cross-validation of the method on 113 carbohydrate-binding domains and 3442 noncarbohydrate binding proteins yields a Matthews correlation coefficient of 0.56 for SPalign alone and 0.63 for SPOT-Struc (SPalign?+?binding affinity scoring) for CBP prediction. SPOT-Struc is a technique with high positive predictive value (79% correct predictions in all positive CBP predictions) with a reasonable sensitivity (52% positive predictions in all CBPs). The sensitivity of the method was changed slightly when applied to 31 APO (unbound) structures found in the protein databank (14/31 for APO versus 15/31 for HOLO). The result of SPOT-Struc will not change significantly if highly homologous templates were used. SPOT-Struc predicted 19 out of 2076 structural genome targets as CBPs. In particular, one uncharacterized protein in Bacillus subtilis (1oq1A) was matched to galectin-9 from Mus musculus. Thus, SPOT-Struc is useful for uncovering novel carbohydrate-binding proteins. SPOT-Struc is available at http://sparks-lab.org.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.format.extent1255925 bytes
dc.format.mimetypeapplication/pdf
dc.languageEnglish
dc.language.isoeng
dc.publisherJohn Wiley & Sons
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationY
dc.relation.ispartofpagefrom2177
dc.relation.ispartofpageto2183
dc.relation.ispartofissue30
dc.relation.ispartofjournalJournal of Computational Chemistry
dc.relation.ispartofvolume35
dc.rights.retentionY
dc.subject.fieldofresearchPhysical chemistry
dc.subject.fieldofresearchTheoretical and computational chemistry
dc.subject.fieldofresearchNanotechnology
dc.subject.fieldofresearchcode3406
dc.subject.fieldofresearchcode3407
dc.subject.fieldofresearchcode4018
dc.titleCarbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.rights.copyright© 2014 Wiley Periodicals, Inc.. This is the accepted version of the following article: Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction, Journal of Computational Chemistry, Vol. 35(30), 2014, pp. 2177-2183, which has been published in final form at dx.doi.org/10.1002/jcc.23730 .
gro.date.issued2015-03-13T04:20:37Z
gro.hasfulltextFull Text
gro.griffith.authorvon Itzstein, Mark


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