{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,8]],"date-time":"2023-10-08T19:28:29Z","timestamp":1696793309373},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Sequence\u2013structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence\u2013structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence\u2013structure alignments ranking) provides a unifying framework for scoring sequence\u2013structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against \u2018standard-of-truth\u2019 structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.<\/jats:p>\n               <jats:p>Availability: The software, examples, the Java documentation and a tutorial are available at<\/jats:p>\n               <jats:p>Contact: \u00a0fabian.birzele@ifi.lmu.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti712","type":"journal-article","created":{"date-parts":[[2005,10,11]],"date-time":"2005-10-11T00:23:46Z","timestamp":1128990226000},"page":"4425-4426","source":"Crossref","is-referenced-by-count":1,"title":["QUASAR\u2014scoring and ranking of sequence\u2013structure alignments"],"prefix":"10.1093","volume":"21","author":[{"given":"Fabian","family":"Birzele","sequence":"first","affiliation":[{"name":"Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University \u00a0 Amalienstrasse 17, D-80333 Munich, Germany"}]},{"given":"Jan E.","family":"Gewehr","sequence":"additional","affiliation":[{"name":"Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University \u00a0 Amalienstrasse 17, D-80333 Munich, Germany"}]},{"given":"Ralf","family":"Zimmer","sequence":"additional","affiliation":[{"name":"Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University \u00a0 Amalienstrasse 17, D-80333 Munich, Germany"}]}],"member":"286","published-online":{"date-parts":[[2005,10,10]]},"reference":[{"key":"2023061007325889500_b1","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":"2023061007325889500_b2","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2105-4-8","article-title":"Amino acid empirical contact energy definitions for fold recognition in the space of contact maps","volume":"4","author":"Berrera","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023061007325889500_b3","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023061007325889500_b4","first-page":"345","article-title":"A model of evolutionary change in proteins","volume":"5","author":"Dayhoff","year":"1978","journal-title":"Atlas Protein Sequence Struct."},{"key":"2023061007325889500_b5","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1093\/nar\/27.1.368","article-title":"AAindex: amino acid index database","volume":"27","author":"Kawashima","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023061007325889500_b6","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1002\/prot.340100307","article-title":"Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities","volume":"10","author":"Luthy","year":"1991","journal-title":"Proteins"},{"key":"2023061007325889500_b7","doi-asserted-by":"crossref","first-page":"215i","DOI":"10.1093\/bioinformatics\/btg1029","article-title":"APDB: a novel measure for benchmarking sequence alignment methods without reference alignments","volume":"19","author":"O'Sullivan","year":"2003","journal-title":"Bioinformatics"},{"key":"2023061007325889500_b8","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/bioinformatics\/16.9.776","article-title":"MaxSub: an automated measure for the assessment of protein structure prediction quality","volume":"16","author":"Siew","year":"2000","journal-title":"Bioinformatics"},{"key":"2023061007325889500_b9","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1093\/protein\/15.9.721","article-title":"Prediction of protein residue contacts with a PDB-derived likelihood matrix","volume":"15","author":"Singer","year":"2002","journal-title":"Protein Eng."},{"key":"2023061007325889500_b10","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K","article-title":"A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment","volume":"34","author":"Zemla","year":"1999","journal-title":"Proteins"},{"key":"2023061007325889500_b11","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Zhang","year":"2004","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4425\/50566312\/bioinformatics_21_24_4425.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4425\/50566312\/bioinformatics_21_24_4425.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T07:33:27Z","timestamp":1686382407000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/24\/4425\/179855"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,10,10]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2005,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti712","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,12,15]]},"published":{"date-parts":[[2005,10,10]]}}}