{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:40Z","timestamp":1740185140255,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,2,14]],"date-time":"2018-02-14T00:00:00Z","timestamp":1518566400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003406","name":"Finnish Funding Agency for Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003406","id-type":"DOI","asserted-by":"publisher"}]},{"name":"THERDIAB","award":["#1843\/31\/2014"],"award-info":[{"award-number":["#1843\/31\/2014"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["290506"],"award-info":[{"award-number":["290506"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>StructureMapper is a high-throughput algorithm for automated mapping of protein primary amino sequence locations to existing three-dimensional protein structures. The algorithm is intended for facilitating easy and efficient utilization of structural information in protein characterization and proteomics. StructureMapper provides an analysis of the identified structural locations that includes surface accessibility, flexibility, protein\u2013protein interfacing, intrinsic disorder prediction, secondary structure assignment, biological assembly information and sequence identity percentages, among other metrics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have showcased the use of the algorithm by estimating the coverage of structural information of the human proteome, identifying critical interface residues in DNA polymerase \u03b3, profiling structurally protease cleavage sites and post-translational modification sites, and by identifying putative, novel phosphoswitches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The StructureMapper algorithm is available as an online service and standalone implementation at http:\/\/structuremapper.uta.fi.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty086","type":"journal-article","created":{"date-parts":[[2018,2,13]],"date-time":"2018-02-13T20:15:58Z","timestamp":1518552958000},"page":"2302-2304","source":"Crossref","is-referenced-by-count":1,"title":["StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data"],"prefix":"10.1093","volume":"34","author":[{"given":"Anssi","family":"Nurminen","sequence":"first","affiliation":[{"name":"Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland"}]},{"given":"Vesa P","family":"Hyt\u00f6nen","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Life Sciences and BioMediTech, University of Tampere, Tampere, Finland"},{"name":"Fimlab Laboratories, Tampere, Finland"}]}],"member":"286","published-online":{"date-parts":[[2018,2,14]]},"reference":[{"key":"2023051604210208000_bty086-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023051604210208000_bty086-B2","doi-asserted-by":"crossref","first-page":"115D","DOI":"10.1093\/nar\/gkh131","article-title":"UniProt: the universal protein knowledgebase","volume":"32","author":"Apweiler","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023051604210208000_bty086-B3","doi-asserted-by":"crossref","first-page":"W604","DOI":"10.1093\/nar\/gkl092","article-title":"Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee","volume":"34","author":"Armougom","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023051604210208000_bty086-B10","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":"2023051604210208000_bty086-B4","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":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051604210208000_bty086-B5","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051604210208000_bty086-B6","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1093\/bioinformatics\/btu744","article-title":"DISOPRED3: precise disordered region predictions with annotated protein-binding activity","volume":"31","author":"Jones","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051604210208000_bty086-B7","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary o f protein secondary structure: pattern recognition of hydrogen bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2023051604210208000_bty086-B8","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1093\/nar\/gkn072","article-title":"PROMALS3D: a tool for multiple protein sequence and structure alignments","volume":"36","author":"Pei","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023051604210208000_bty086-B9","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/0022-2836(73)90011-9","article-title":"Environment and exposure to solvent of protein atoms. Lysozyme and insulin","volume":"15","author":"Shrake","year":"1973","journal-title":"J. Mol. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/13\/2302\/50315932\/bioinformatics_34_13_2302.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/13\/2302\/50315932\/bioinformatics_34_13_2302.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T04:22:16Z","timestamp":1684210936000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/13\/2302\/4857361"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,2,14]]},"references-count":10,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2018,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty086","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,7,1]]},"published":{"date-parts":[[2018,2,14]]}}}