SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence

dc.contributor.author Jia, Kejue
dc.contributor.author Jernigan, Robert
dc.contributor.author Jernigan, Robert
dc.contributor.department Biochemistry, Biophysics and Molecular Biology
dc.contributor.department Bioinformatics and Computational Biology
dc.date 2018-10-06T09:53:01.000
dc.date.accessioned 2020-06-29T23:46:21Z
dc.date.available 2020-06-29T23:46:21Z
dc.date.copyright Mon Jan 01 00:00:00 UTC 2018
dc.date.issued 2018-02-21
dc.description.abstract <p>Protein sequence matching does not properly account for some well-known features of protein structures: surface residues being more variable than core residues, the high packing densities in globular proteins, and does not yield good matches of sequences of many proteins known to be close structural relatives. There are now abundant protein sequences and structures to enable major improvements to sequence matching. Here, we utilize structural frameworks to mount the observed correlated sequences to identify the most important correlated parts. The rationale is that protein structures provide the important physical framework for improving sequence matching. Combining the sequence and structure data in this way leads to a simple amino acid substitution matrix that can be readily incorporated into any sequence matching. This enables the incorporation of allosteric information into sequence matching and transforms it effectively from a 1-D to a 3-D procedure. The results from testing in over 3,000 sequence matches demonstrate a 37% gain in sequence similarity and a loss of 26% of the gaps when compared with the use of BLOSUM62. And, importantly there are major gains in the specificity of sequence matching across diverse proteins. Specifically, all known cases where protein structures match but sequences do not match well are resolved.</p>
dc.description.comments <p>This is a preprint made available through bioRxiv: doi: <a href="http://dx.doi.org/10.1101/268904" target="_blank">10.1101/268904</a>.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/bbmb_ag_pubs/195/
dc.identifier.articleid 1204
dc.identifier.contextkey 12926815
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath bbmb_ag_pubs/195
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/10660
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/bbmb_ag_pubs/195/2018_Jernigan_SeqStructPreprint.pdf|||Fri Jan 14 21:57:18 UTC 2022
dc.source.uri 10.1101/268904
dc.subject.disciplines Biochemistry
dc.subject.disciplines Biophysics
dc.subject.disciplines Molecular Biology
dc.subject.disciplines Structural Biology
dc.title SeqStruct : A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence
dc.type article
dc.type.genre article
dspace.entity.type Publication
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relation.isOrgUnitOfPublication c331f825-0643-499a-9eeb-592c7b43b1f5
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