{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,8]],"date-time":"2024-07-08T21:17:09Z","timestamp":1720473429714},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-13-259","type":"journal-article","created":{"date-parts":[[2012,10,7]],"date-time":"2012-10-07T00:14:48Z","timestamp":1349568888000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment"],"prefix":"10.1186","volume":"13","author":[{"given":"Noah M","family":"Daniels","sequence":"first","affiliation":[]},{"given":"Shilpa","family":"Nadimpalli","sequence":"additional","affiliation":[]},{"given":"Lenore J","family":"Cowen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,10,6]]},"reference":[{"issue":"3","key":"5705_CR1","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/j.sbi.2009.04.003","volume":"19","author":"H Hasegawa","year":"2009","unstructured":"Hasegawa H, Holm L: Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 2009, 19(3):341\u2013348. 10.1016\/j.sbi.2009.04.003","journal-title":"Curr Opin Struct Biol"},{"issue":"3","key":"5705_CR2","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1093\/nar\/29.3.638","volume":"29","author":"NV Grishin","year":"2001","unstructured":"Grishin NV: KH domain: one motif, two folds. Nucleic Acids Res 2001, 29(3):638\u2013643. 10.1093\/nar\/29.3.638","journal-title":"Nucleic Acids Res"},{"key":"5705_CR3","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.jmb.2004.04.058","volume":"340","author":"O O\u2019Sullivan","year":"2004","unstructured":"O\u2019Sullivan O, Suhre K, Abergel C, Higgins D, Notredame C: 3DCoffee: combining protein sequences and structures with multiple sequence alignments. J Mol Biol 2004, 340: 385\u2013395. 10.1016\/j.jmb.2004.04.058","journal-title":"J Mol Biol"},{"key":"5705_CR4","doi-asserted-by":"publisher","first-page":"2295","DOI":"10.1093\/nar\/gkn072","volume":"36","author":"J Pei","year":"2008","unstructured":"Pei J, Kim BH, Grishin NV: PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 2008, 36: 2295\u20132300. 10.1093\/nar\/gkn072","journal-title":"Nucleic Acids Res"},{"key":"5705_CR5","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1093\/protein\/gzp040","volume":"22","author":"M Madhusudhan","year":"2009","unstructured":"Madhusudhan M, Webb BM, Marti-Renom MA, Eswar N, Sali A: Alignment of multiple protein structures based on sequence and structure features. Protein Engineering, Design and Selection 2009, 22: 569\u2013574. 10.1093\/protein\/gzp040","journal-title":"Protein Engineering, Design and Selection"},{"key":"5705_CR6","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1186\/1471-2105-8-355","volume":"8","author":"C Kim","year":"2007","unstructured":"Kim C, Lee B: Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinf 2007, 8: 355. 10.1186\/1471-2105-8-355","journal-title":"BMC Bioinf"},{"key":"5705_CR7","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.1371\/journal.pcbi.0040010","volume":"4","author":"M Menke","year":"2008","unstructured":"Menke M, Berger B, Cowen L: Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol 2008, 4: e10. 10.1371\/journal.pcbi.0040010","journal-title":"PLoS Comput Biol"},{"key":"5705_CR8","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1007\/978-3-642-13078-6_4","volume":"6053\/2010","author":"N Daniels","year":"2010","unstructured":"Daniels N, Kumar A, Cowen L, Menke M: Touring protein space with Matt. Bioinf Res App 2010, 6053\/2010: 18\u201328. http:\/\/www.springerlink.com\/index\/q9j12472213qtx28.pdf","journal-title":"Bioinf Res App"},{"key":"5705_CR9","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1002\/prot.20921","volume":"64","author":"A Konagurthu","year":"2006","unstructured":"Konagurthu A, Whisstock J, Stuckey P, Lesk A: MUSTANG: A multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics 2006, 64: 559\u2013574. 10.1002\/prot.20921","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"5705_CR10","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame C, Higgins D, Heringa J: T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302: 205\u2013217. 10.1006\/jmbi.2000.4042","journal-title":"J Mol Biol"},{"key":"5705_CR11","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1093\/bioinformatics\/bth493","volume":"21","author":"I VanWalle","year":"2005","unstructured":"VanWalle I, Lasters I, Wyns L: SABmark\u2013a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21: 1267\u20131268. 10.1093\/bioinformatics\/bth493","journal-title":"Bioinformatics"},{"key":"5705_CR12","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1002\/prot.20665","volume":"62","author":"M Shatsky","year":"2006","unstructured":"Shatsky M, Nussinov R, Wolfson H: Optimization of multiple-sequence alignment based on multiple-structure alignment. Proteins: Structure, Function and Bioinformatics 2006, 62: 209\u2013217.","journal-title":"Proteins: Structure, Function and Bioinformatics"},{"key":"5705_CR13","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22: 4673\u20134680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"key":"5705_CR14","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"R Edgar","year":"2004","unstructured":"Edgar R: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792\u20131797. 10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"5705_CR15","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1101\/gr.2821705","volume":"15","author":"C Do","year":"2005","unstructured":"Do C, Mahabhashyam M, Brudno M, Batzoglou S: ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15: 220\u2013240.","journal-title":"Genome Res"},{"key":"5705_CR16","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1093\/bib\/bbn013","volume":"9","author":"K Katoh","year":"2008","unstructured":"Katoh K, Toh H: Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 2008, 9: 286\u2013298. 10.1093\/bib\/bbn013","journal-title":"Briefings in Bioinformatics"},{"key":"5705_CR17","doi-asserted-by":"publisher","first-page":"2469","DOI":"10.1002\/pro.5560071126","volume":"11","author":"K Mizuguchi","year":"1998","unstructured":"Mizuguchi K, Deane C, Blundell TL, Overington J: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998, 11: 2469\u20132471.","journal-title":"Protein Sci"},{"key":"5705_CR18","doi-asserted-by":"publisher","first-page":"i287","DOI":"10.1093\/bioinformatics\/btq199","volume":"26","author":"A Kumar","year":"2010","unstructured":"Kumar A, Cowen L: Recognition of beta structural motifs using hidden Markov models trained with simulated evolution. Bioinformatics 2010, 26: i287-i293. 10.1093\/bioinformatics\/btq199","journal-title":"Bioinformatics"},{"key":"5705_CR19","doi-asserted-by":"publisher","first-page":"4069","DOI":"10.1073\/pnas.0909950107","volume":"107","author":"M Menke","year":"2010","unstructured":"Menke M, Berger B, Cowen L: Markov random fields reveal an N-terminal double propeller motif as part of a bacterial hybrid two-component sensor system. PNAS 2010, 107: 4069\u20134074. 10.1073\/pnas.0909950107","journal-title":"PNAS"},{"issue":"9","key":"5705_CR20","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1093\/bioinformatics\/bts110","volume":"28","author":"NM Daniels","year":"2012","unstructured":"Daniels NM, Hosur R, Berger B, Cowen LJ: SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. Bioinformatics 2012, 28(9):1216\u20131222. 10.1093\/bioinformatics\/bts110","journal-title":"Bioinformatics"},{"key":"5705_CR21","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1002\/prot.10100","volume":"48","author":"M Shatsky","year":"2002","unstructured":"Shatsky M, Nussinov R, Wolfson H: Flexible protein alignment and hinge detection. Proteins 2002, 48: 242\u2013256. 10.1002\/prot.10100","journal-title":"Proteins"},{"key":"5705_CR22","doi-asserted-by":"crossref","first-page":"II246","DOI":"10.1093\/bioinformatics\/btg1086","volume":"Suppl 2","author":"Y Ye","year":"2003","unstructured":"Ye Y, Godzik A: Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, Suppl 2: II246-II255.","journal-title":"Bioinformatics"},{"key":"5705_CR23","doi-asserted-by":"publisher","first-page":"2362","DOI":"10.1093\/bioinformatics\/bti353","volume":"21","author":"Y Ye","year":"2005","unstructured":"Ye Y, Godzik A: Multiple flexible structure alignment using partial order graphs. Bioinformatics 2005, 21: 2362\u20132369. 10.1093\/bioinformatics\/bti353","journal-title":"Bioinformatics"},{"key":"5705_CR24","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1186\/1471-2105-9-352","volume":"9","author":"R Mosca","year":"2008","unstructured":"Mosca R, Brannetti B, Schneider TR: Alignment of protein structures in the presence of domain motions. BMC Bioinformatics 2008, 9: 352. 10.1186\/1471-2105-9-352","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"5705_CR25","first-page":"1","volume":"12","author":"S Salem","year":"2010","unstructured":"Salem S, Zaki MJ, Bystroff C: FlexSnap: Flexible non-sequential protein structure alignment. Algorithms Mol Biol 2010, 12(5):1\u201313.","journal-title":"Algorithms Mol Biol"},{"key":"5705_CR26","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","volume":"14","author":"S Eddy","year":"1998","unstructured":"Eddy S: Profile hidden Markov models. Bioinformatics 1998, 14: 755\u2013763. 10.1093\/bioinformatics\/14.9.755","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-259.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T03:24:49Z","timestamp":1687749889000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-259"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,10,6]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5705"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-259","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,10,6]]},"assertion":[{"value":"10 May 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 October 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"259"}}