3D-blast: 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations.
Identifieur interne : 000113 ( PubMed/Corpus ); précédent : 000112; suivant : 0001143D-blast: 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations.
Auteurs : Lazaros Mavridis ; David W. RitchieSource :
- Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing [ 2335-6936 ] ; 2010.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- chemical , classification : Proteins.
- Cluster Analysis, Computational Biology, Databases, Protein, Fourier Analysis, Models, Molecular, Protein Conformation, Protein Interaction Domains and Motifs, Software, Structural Homology, Protein.
Abstract
This paper presents a novel sequence-independent method of aligning protein structures using three-dimensional spherical polar Fourier (SPF) representations of protein shape. The approach is demonstrated by clustering subsets of the CATH database for each of the four main CATH fold types, and by searching the entire CATH database of some 12,000 structures using several protein structures as queries. Overall, the automatic SPF clustering approach agrees very well with the expert-curated CATH classification, and ROC plot analyses of the database searches show that the approach has very high precision and recall. Database query times can be reduced considerably by using a simple rotationally-invariant pre-filter in tandem with a more sensitive rotational search with little or no reduction in accuracy. Hence it should soon be possible to perform on-line 3D structural searches in interactive time-scales.
PubMed: 19908380
Links to Exploration step
pubmed:19908380Le document en format XML
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Ritchie</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:19908380</idno><idno type="pmid">19908380</idno><idno type="wicri:Area/PubMed/Corpus">000113</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000113</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">3D-blast: 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations.</title><author><name sortKey="Mavridis, Lazaros" sort="Mavridis, Lazaros" uniqKey="Mavridis L" first="Lazaros" last="Mavridis">Lazaros Mavridis</name><affiliation><nlm:affiliation>INRIA Nancy - Grand Est, LORIA, 615 rue du Jardin Botanique, 54506 Vandoeuvre-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name></author></analytic><series><title level="j">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</title><idno type="ISSN">2335-6936</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cluster Analysis</term><term>Computational Biology</term><term>Databases, Protein</term><term>Fourier Analysis</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Protein Interaction Domains and Motifs</term><term>Proteins (chemistry)</term><term>Proteins (classification)</term><term>Software</term><term>Structural Homology, Protein</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Computational Biology</term><term>Databases, Protein</term><term>Fourier Analysis</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Protein Interaction Domains and Motifs</term><term>Software</term><term>Structural Homology, Protein</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">This paper presents a novel sequence-independent method of aligning protein structures using three-dimensional spherical polar Fourier (SPF) representations of protein shape. The approach is demonstrated by clustering subsets of the CATH database for each of the four main CATH fold types, and by searching the entire CATH database of some 12,000 structures using several protein structures as queries. Overall, the automatic SPF clustering approach agrees very well with the expert-curated CATH classification, and ROC plot analyses of the database searches show that the approach has very high precision and recall. Database query times can be reduced considerably by using a simple rotationally-invariant pre-filter in tandem with a more sensitive rotational search with little or no reduction in accuracy. Hence it should soon be possible to perform on-line 3D structural searches in interactive time-scales.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">19908380</PMID><DateCreated><Year>2009</Year><Month>11</Month><Day>12</Day></DateCreated><DateCompleted><Year>2013</Year><Month>11</Month><Day>13</Day></DateCompleted><Article PubModel="Print"><Journal><ISSN IssnType="Print">2335-6936</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2010</Year></PubDate></JournalIssue><Title>Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</Title><ISOAbbreviation>Pac Symp Biocomput</ISOAbbreviation></Journal><ArticleTitle>3D-blast: 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations.</ArticleTitle><Pagination><MedlinePgn>281-92</MedlinePgn></Pagination><Abstract><AbstractText>This paper presents a novel sequence-independent method of aligning protein structures using three-dimensional spherical polar Fourier (SPF) representations of protein shape. The approach is demonstrated by clustering subsets of the CATH database for each of the four main CATH fold types, and by searching the entire CATH database of some 12,000 structures using several protein structures as queries. Overall, the automatic SPF clustering approach agrees very well with the expert-curated CATH classification, and ROC plot analyses of the database searches show that the approach has very high precision and recall. Database query times can be reduced considerably by using a simple rotationally-invariant pre-filter in tandem with a more sensitive rotational search with little or no reduction in accuracy. 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