{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T08:09:31Z","timestamp":1778659771228,"version":"3.51.4"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: To efficiently analyze the \u2018native ensemble of conformations\u2019 accessible to proteins near their folded state and to extract essential information from observed distributions of conformations, reliable mathematical methods and computational tools are needed.<\/jats:p>\n               <jats:p>Result: Examination of 24 pairs of structures determined by both NMR and X-ray reveals that the differences in the dynamics of the same protein resolved by the two techniques can be tracked to the most robust low frequency modes elucidated by principal component analysis (PCA) of NMR models. The active sites of enzymes are found to be highly constrained in these PCA modes. Furthermore, the residues predicted to be highly immobile are shown to be evolutionarily conserved, lending support to a PCA-based identification of potential functional sites. An online tool, PCA_NEST, is designed to derive the principal modes of conformational changes from structural ensembles resolved by experiments or generated by computations.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/ignm.ccbb.pitt.edu\/oPCA_Online.htm<\/jats:p>\n               <jats:p>Contact: \u00a0lwy1@iam.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp023","type":"journal-article","created":{"date-parts":[[2009,1,16]],"date-time":"2009-01-16T01:44:59Z","timestamp":1232070299000},"page":"606-614","source":"Crossref","is-referenced-by-count":125,"title":["Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics"],"prefix":"10.1093","volume":"25","author":[{"given":"Lee-Wei","family":"Yang","sequence":"first","affiliation":[{"name":"1 University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan, 2University of Pittsburgh, School of Medicine, Department of Computational Biology, PA, USA and 3Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eran","family":"Eyal","sequence":"additional","affiliation":[{"name":"1 University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan, 2University of Pittsburgh, School of Medicine, Department of Computational Biology, PA, USA and 3Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivet","family":"Bahar","sequence":"additional","affiliation":[{"name":"1 University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan, 2University of Pittsburgh, School of Medicine, Department of Computational Biology, PA, USA and 3Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akio","family":"Kitao","sequence":"additional","affiliation":[{"name":"1 University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan, 2University of Pittsburgh, School of Medicine, Department of Computational Biology, PA, USA and 3Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Japan"},{"name":"1 University of Tokyo, Institute of Molecular and Cellular Bioscience, Tokyo, Japan, 2University of Pittsburgh, School of Medicine, Department of Computational Biology, PA, USA and 3Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,15]]},"reference":[{"key":"2023013110115404800_B1","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1110\/ps.04882105","article-title":"Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool","volume":"14","author":"Alexandrov","year":"2005","journal-title":"Protein Sci."},{"key":"2023013110115404800_B2","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/prot.340170408","article-title":"Essential dynamics of proteins","volume":"17","author":"Amadei","year":"1993","journal-title":"Proteins"},{"key":"2023013110115404800_B3","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1002\/prot.21507","article-title":"A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing","volume":"69","author":"Andrec","year":"2007","journal-title":"Proteins"},{"key":"2023013110115404800_B4","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/S0006-3495(01)76033-X","article-title":"Anisotropy of fluctuation dynamics of proteins with an elastic network model","volume":"80","author":"Atilgan","year":"2001","journal-title":"Biophys. 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