{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:31Z","timestamp":1772138071329,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,16]],"date-time":"2024-12-16T00:00:00Z","timestamp":1734307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Beta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play many key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated with each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify a single amino acid (e.g. aspartic acid at turn position 1) have been systematically investigated. Furthermore, no general evaluation has been made of the SC interactions between turns and their BB neighborhoods. Finally, the visualization and comparison of the wide range of turn conformations has been hampered by the almost exclusive characterization of turn structure in BB dihedral-angle (Ramachandran) space.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>This work introduces MapTurns, a web server for motif maps, which employ a turn-local Euclidean-space coordinate system and a global turn alignment to comprehensively map the distributions of BB and SC structure and H-bonding associated with sequence motifs in beta turns and their local BB contexts. Maps characterize many new SC motifs, provide detailed rationalizations of sequence preferences, and support mutational analysis and the general study of SC interactions, and they should prove useful in applications such as protein design.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>MapTurns is available at www.betaturn.com. Sample code is available at: https:\/\/github.com\/nenewell\/MapTurns\/tree\/main.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae741","type":"journal-article","created":{"date-parts":[[2024,12,13]],"date-time":"2024-12-13T07:26:47Z","timestamp":1734074807000},"source":"Crossref","is-referenced-by-count":2,"title":["MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8920-7750","authenticated-orcid":false,"given":"Nicholas E","family":"Newell","sequence":"first","affiliation":[{"name":"Independent Scientist , Reading, MA 01867,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,12,16]]},"reference":[{"key":"2024122621363843900_btae741-B1","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/pro.5560070103","article-title":"Helix capping","volume":"7","author":"Aurora","year":"1998","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2024122621363843900_btae741-B3","volume-title":"Discrete Multivariate Analysis: Theory and Practice","year":"2007"},{"key":"2024122621363843900_btae741-B4","doi-asserted-by":"crossref","first-page":"e4868","DOI":"10.1002\/pro.4868","article-title":"Emerging role of carbonyl-carbonyl interactions in the classification of beta turns","volume":"33","author":"D\u2019Arminio","year":"2024","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B5","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1002\/pro.4020","article-title":"A systematic analysis of the beta hairpin motif in the Protein Data Bank","volume":"30","author":"DuPai","year":"2021","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B6","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1002\/bmb.2006.494034042644","article-title":"Biomolecules in the computer: jmol to the rescue","volume":"34","author":"Herr\u00e1ez","year":"2006","journal-title":"Biochem Mol Biol Educ"},{"key":"2024122621363843900_btae741-B7","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":"Hollingsworth","year":"2010","journal-title":"Biomol Concepts"},{"key":"2024122621363843900_btae741-B8","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1002\/pro.5560020701","article-title":"Probing the roles of residues at the e and g positions of the GCN4 leucine zipper by combinatorial mutagenesis","volume":"2","author":"Hu","year":"1993","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B9","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1002\/pro.5560050204","article-title":"PROMOTIF\u2014a program to identify and analyze structural motifs in proteins","volume":"5","author":"Hutchinson","year":"1996","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B10","first-page":"68","volume-title":"Finding Groups in Data: An Introduction to Cluster Analysis","author":"Kaufman","year":"2005"},{"key":"2024122621363843900_btae741-B12","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0167-4838(87)90017-3","article-title":"Beta-bulges within loops as recurring features of protein structure","volume":"911","author":"Milner-White","year":"1987","journal-title":"Biochim Biophys Acta"},{"key":"2024122621363843900_btae741-B13","doi-asserted-by":"publisher","author":"Newell","year":"2024","DOI":"10.1101\/2024.01.01.573820"},{"key":"2024122621363843900_btae741-B14","doi-asserted-by":"crossref","first-page":"e5159","DOI":"10.1002\/pro.5159","article-title":"Geometric descriptors for beta turns","volume":"33","author":"Newell","year":"2024","journal-title":"Protein Sci"},{"key":"2024122621363843900_btae741-B15","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1186\/s12859-015-0671-4","article-title":"Mapping side chain interactions at protein helix termini","volume":"16","author":"Newell","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2024122621363843900_btae741-B16","first-page":"53","volume-title":"Protein Folding","author":"Schellman","year":"1980"},{"key":"2024122621363843900_btae741-B17","doi-asserted-by":"crossref","first-page":"e1006844","DOI":"10.1371\/journal.pcbi.1006844","article-title":"A new clustering and nomenclature for beta turns derived from high-resolution protein structures","volume":"15","author":"Shapovalov","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2024122621363843900_btae741-B18","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1002\/bip.1968.360061006","article-title":"Stereochemical criteria for polypeptides and proteins. 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