{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T23:19:11Z","timestamp":1782343151617,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006844","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,19]],"date-time":"2019-03-19T00:00:00Z","timestamp":1552953600000}}],"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2019,3,7]],"date-time":"2019-03-07T00:00:00Z","timestamp":1551916800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM122517"],"award-info":[{"award-number":["R35 GM122517"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006844","type":"journal-article","created":{"date-parts":[[2019,3,7]],"date-time":"2019-03-07T14:33:30Z","timestamp":1551969210000},"page":"e1006844","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":85,"title":["A new clustering and nomenclature for beta turns derived from high-resolution protein structures"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9349-7647","authenticated-orcid":true,"given":"Maxim","family":"Shapovalov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Slobodan","family":"Vucetic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7674-6667","authenticated-orcid":true,"given":"Roland L.","family":"Dunbrack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,3,7]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1002\/bip.1968.360061006","article-title":"Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units","volume":"6","author":"C. Venkatachalam","year":"1968","journal-title":"Biopolymers"},{"key":"ref2","first-page":"167","article-title":"Adv. Protein Chem","author":"J.S. Richardson","year":"1981"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/0022-2836(88)90103-9","article-title":"Analysis and prediction of the different types of \u03b2-turn in proteins","volume":"203","author":"C. Wilmot","year":"1988","journal-title":"J. Mol. Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/protein\/3.6.479","article-title":"Beta-turns and their distortions: a proposed new nomenclature","volume":"3","author":"C.M. Wilmot","year":"1990","journal-title":"Protein Eng"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1002\/prot.22185","article-title":"Turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions","volume":"74","author":"O. Koch","year":"2009","journal-title":"Proteins"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/abio.2000.4757","article-title":"Prediction of tight turns and their types in proteins","volume":"286","author":"K.-C. Chou","year":"2000","journal-title":"Anal. Biochem"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"4009","DOI":"10.1021\/ja00766a060","article-title":"Protein folding","volume":"94","author":"I. Kuntz","year":"1972","journal-title":"J. Am. Chem. Soc"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1038\/272586a0","article-title":"Prediction of chain turns in globular proteins on a hydrophobic basis","volume":"272","author":"G.D. Rose","year":"1978","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1002\/bip.20960","article-title":"Roles of \u03b2\u2010turns in protein folding: From peptide models to protein engineering","volume":"89","author":"A.M.C. Marcelino","year":"2008","journal-title":"Biopolymers"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"W. Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/ijch.197300017","article-title":"Energy parameters in polypeptides. VI. Conformational energy analysis of the N-Acetyl N&apos;-methyl amides of the twenty naturally occurring amino acids","volume":"11","author":"P.N. Lewis","year":"1973","journal-title":"Israeli Journal of Chemistry"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/S0022-2836(02)01338-4","article-title":"Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation","volume":"326","author":"L. Pal","year":"2003","journal-title":"J. Mol. Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1110\/ps.8.5.1045","article-title":"Prediction of the location and type of \u03b2-turns in proteins using neural networks","volume":"8","author":"A.J. Shepherd","year":"1999","journal-title":"Protein Sci"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1110\/ps.0228903","article-title":"Prediction of \u03b2\u2010turns in proteins from multiple alignment using neural network","volume":"12","author":"H. Kaur","year":"2003","journal-title":"Protein Sci"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1186\/1471-2105-11-407","article-title":"Predicting \u03b2-turns and their types using predicted backbone dihedral angles and secondary structures","volume":"11","author":"P. Kountouris","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1002\/prot.22164","article-title":"Prediction of turn types in protein structure by machine-learning classifiers","volume":"74","author":"M. Meissner","year":"2009","journal-title":"Proteins"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1002\/pro.5560031206","article-title":"A revised set of potentials for beta-turn formation in proteins","volume":"3","author":"E.G. Hutchinson","year":"1994","journal-title":"Protein Sci"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1002\/prot.20461","article-title":"High accuracy prediction of \u03b2\u2010turns and their types using propensities and multiple alignments","volume":"59","author":"P.F. Fuchs","year":"2005","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"153","DOI":"10.6026\/97320630001153","article-title":"Protein beta-turn assignments","volume":"1","author":"A. Bornot","year":"2006","journal-title":"Bioinformation"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"33191","DOI":"10.1038\/srep33191","article-title":"Extension of the classical classification of \u03b2-turns","volume":"6","author":"A.G. de Brevern","year":"2016","journal-title":"Scientific reports"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1002\/pro.5560060125","article-title":"Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability","volume":"6","author":"E.C. Ohage","year":"1997","journal-title":"Protein Sci"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/BF03404909","article-title":"Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials","volume":"25","author":"K. Guruprasad","year":"2000","journal-title":"J. Biosci. (Bangalore)"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1000763","DOI":"10.1371\/journal.pcbi.1000763","article-title":"Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model","volume":"6","author":"D. Ting","year":"2010","journal-title":"PLOS Comput. Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1093\/bioinformatics\/btw823","article-title":"Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction","volume":"33","author":"C. Marks","year":"2017","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.jmb.2010.10.030","article-title":"A new clustering of antibody CDR loop conformations","volume":"406","author":"B. North","year":"2011","journal-title":"J. Mol. Biol"},{"key":"ref26","unstructured":"M. Ester, H.-P. Kriegel, J. Sander, X. Xu. A density-based algorithm for discovering clusters in large spatial databases with noise. in Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96). 1996. Association for the Advancement of Artificial Intelligence."},{"key":"ref27","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1515\/bmc.2010.022","article-title":"A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins","volume":"1","author":"S.A. Hollingsworth","year":"2010","journal-title":"Biomolecular concepts"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","article-title":"PISCES: a protein sequence culling server","volume":"19","author":"G. Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"W94","DOI":"10.1093\/nar\/gki402","article-title":"PISCES: recent improvements to a PDB sequence culling server","volume":"33","author":"G. Wang","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/S0022-2836(05)80329-8","article-title":"Situations of gamma-turns in proteins: Their relation to alpha-helices, beta-sheets and ligand binding sites","volume":"216","author":"E.J. Milner-White","year":"1990","journal-title":"J. Mol. Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1002\/pro.5560050719","article-title":"Experimentally observed conformation-dependent geometry and hidden strain in proteins","volume":"5","author":"P.A. Karplus","year":"1996","journal-title":"Protein Sci"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/prot.20064","article-title":"Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding","volume":"55","author":"B. Dasgupta","year":"2004","journal-title":"Proteins: Structure, Function and Genetics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.jmb.2011.12.022","article-title":"(phi,psi)(2) Motifs: A Purely Conformation-Based Fine-Grained Enumeration of Protein Parts at the Two-Residue Level","volume":"416","author":"S.A. Hollingsworth","year":"2012","journal-title":"J. Mol. Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/prot.10286","article-title":"Structure validation by Calpha geometry: phi,psi and Cbeta deviation","volume":"50","author":"S.C. Lovell","year":"2003","journal-title":"Proteins: Structure, Function and Genetics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2437","DOI":"10.1021\/acs.jcim.7b00391","article-title":"Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures","volume":"57","author":"A. Meyder","year":"2017","journal-title":"Journal of chemical information and modeling"},{"key":"ref36","doi-asserted-by":"crossref","unstructured":"Y. Liu, Z. Li, H. Xiong, X. Gao, J. Wu. Understanding of internal clustering validation measures. in Data Mining (ICDM), 2010 IEEE 10th International Conference on. 2010. IEEE.","DOI":"10.1109\/ICDM.2010.35"},{"key":"ref37","doi-asserted-by":"crossref","unstructured":"D. Moulavi, P.A. Jaskowiak, R.J. Campello, A. Zimek, J. Sander. Density-based clustering validation. in Proceedings of the 2014 SIAM International Conference on Data Mining. 2014. SIAM.","DOI":"10.1137\/1.9781611973440.96"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"P.J. Rousseeuw","year":"1987","journal-title":"Journal of computational and applied mathematics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/S0006-3495(79)85259-5","article-title":"Prediction of beta-turns","volume":"26","author":"P. Chou","year":"1979","journal-title":"Biophys. J"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1002\/bip.20266","article-title":"3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation","volume":"78","author":"L. Pal","year":"2005","journal-title":"Biopolymers"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1006\/jmbi.1999.3217","article-title":"Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations","volume":"294","author":"D. Pal","year":"1999","journal-title":"J. Mol. Biol"},{"key":"ref42","article-title":"Real-space refinement in PHENIX for cryo-EM and crystallography","volume":"74","author":"P.V. Afonine","year":"2018","journal-title":"Acta Crystallographica Section D: Structural Biology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1016\/S0006-3495(02)75315-0","article-title":"Addition of missing loops and domains to protein models by x-ray solution scattering","volume":"83","author":"M.V. Petoukhov","year":"2002","journal-title":"Biophys. J"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e113811","DOI":"10.1371\/journal.pone.0113811","article-title":"Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments","volume":"9","author":"H. Park","year":"2014","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e1003539","DOI":"10.1371\/journal.pcbi.1003539","article-title":"Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method","volume":"10","author":"K. Tang","year":"2014","journal-title":"PLOS Comput. Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1186\/s13059-014-0484-1","article-title":"Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations","volume":"15","author":"L.G. Martelotto","year":"2014","journal-title":"Genome biology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.sbi.2015.01.003","article-title":"Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins","volume":"32","author":"T.G. Kucukkal","year":"2015","journal-title":"Curr. Opin. Struct. Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM-HMM comparison","volume":"21","author":"J. S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"key":"ref49","article-title":"Wiley Series in Probability and Statistics","author":"K.V. Mardia","year":"2000"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.str.2011.03.019","article-title":"A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions","volume":"19","author":"M.V. Shapovalov","year":"2011","journal-title":"Structure"},{"key":"ref51","first-page":"2825","article-title":"Scikit-learn: Machine learning in Python","volume":"12","author":"F. Pedregosa","year":"2011","journal-title":"Journal of machine learning research"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"P.J. Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gku1028","article-title":"A series of PDB-related databanks for everyday needs","volume":"43","author":"W.G. Touw","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref54","unstructured":"E. Jones, T. Oliphant, P. Peterson. SciPy: Open source scientific tools for Python. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.scipy.org\" xlink:type=\"simple\">http:\/\/www.scipy.org<\/ext-link>"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006844","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,19]],"date-time":"2019-03-19T00:00:00Z","timestamp":1552953600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006844","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T02:39:47Z","timestamp":1694659187000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006844"}},"subtitle":[],"editor":[{"given":"Charlotte M.","family":"Deane","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,3,7]]},"references-count":54,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,3,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006844","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/390211","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,7]]}}}