{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T01:23:10Z","timestamp":1777598590528,"version":"3.51.4"},"reference-count":28,"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":[[2014,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful\/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>ProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker\u2019s JESS motif set [Bioinformatics 19:1644\u20131649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program\u2019s usability and speed, and have improved the way that the results are presented.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-15-87","type":"journal-article","created":{"date-parts":[[2014,3,27]],"date-time":"2014-03-27T02:03:40Z","timestamp":1395885820000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Estimation of protein function using template-based alignment of enzyme active sites"],"prefix":"10.1186","volume":"15","author":[{"given":"Brett","family":"Hanson","sequence":"first","affiliation":[]},{"given":"Charles","family":"Westin","sequence":"additional","affiliation":[]},{"given":"Mario","family":"Rosa","sequence":"additional","affiliation":[]},{"given":"Alexander","family":"Grier","sequence":"additional","affiliation":[]},{"given":"Mikhail","family":"Osipovitch","sequence":"additional","affiliation":[]},{"given":"Madolyn L","family":"MacDonald","sequence":"additional","affiliation":[]},{"given":"Greg","family":"Dodge","sequence":"additional","affiliation":[]},{"given":"Paule M","family":"Boli","sequence":"additional","affiliation":[]},{"given":"Cyprian W","family":"Corwin","sequence":"additional","affiliation":[]},{"given":"Haeja","family":"Kessler","sequence":"additional","affiliation":[]},{"given":"Talia","family":"McKay","sequence":"additional","affiliation":[]},{"given":"Herbert J","family":"Bernstein","sequence":"additional","affiliation":[]},{"given":"Paul A","family":"Craig","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,3,27]]},"reference":[{"key":"6341_CR1","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/j.jmb.2005.01.044","volume":"347","author":"JW Torrance","year":"2005","unstructured":"Torrance JW, Bartlett GJ, Porter CT, Thornton JM: Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol. 2005, 347: 565-581. 10.1016\/j.jmb.2005.01.044.","journal-title":"J Mol Biol"},{"key":"6341_CR2","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.cbpa.2003.11.001","volume":"8","author":"S Jones","year":"2004","unstructured":"Jones S, Thornton JM: Searching for functional sites in protein structures. Curr Opin Chem Biol. 2004, 8: 3-7. 10.1016\/j.cbpa.2003.11.001.","journal-title":"Curr Opin Chem Biol"},{"key":"6341_CR3","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bib\/bbl004","volume":"7","author":"I Friedberg","year":"2006","unstructured":"Friedberg I: Automated protein function prediction\u2014the genomic challenge. Brief Bioinform. 2006, 7: 225-242. 10.1093\/bib\/bbl004.","journal-title":"Brief Bioinform"},{"key":"6341_CR4","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/S0167-7799(99)01398-0","volume":"18","author":"J Skolnick","year":"2000","unstructured":"Skolnick J, Fetrow JS: From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol. 2000, 18: 34-39. 10.1016\/S0167-7799(99)01398-0.","journal-title":"Trends Biotechnol"},{"key":"6341_CR5","doi-asserted-by":"publisher","first-page":"9950","DOI":"10.1021\/bi201312u","volume":"50","author":"JA Gerlt","year":"2011","unstructured":"Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV: The enzyme function initiative. Biochemistry. 2011, 50: 9950-9962. 10.1021\/bi201312u.","journal-title":"Biochemistry"},{"key":"6341_CR6","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: 341-348. 10.1016\/j.sbi.2009.04.003.","journal-title":"Curr Opin Struct Biol"},{"key":"6341_CR7","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093\/nar\/25.17.3389.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR8","doi-asserted-by":"publisher","first-page":"3986","DOI":"10.1093\/nar\/26.17.3986","volume":"26","author":"Z Zhang","year":"1998","unstructured":"Zhang Z, Miller W, Sch\u00e4ffer AA, Madden TL, Lipman DJ, Koonin EV, Altschul SF: Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. 1998, 26: 3986-3990. 10.1093\/nar\/26.17.3986.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR9","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1016\/S0076-6879(96)66041-8","volume":"266","author":"L Holm","year":"1996","unstructured":"Holm L, Sander C: Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol. 1996, 266: 653-662.","journal-title":"Methods Enzymol"},{"key":"6341_CR10","doi-asserted-by":"publisher","first-page":"D465","DOI":"10.1093\/nar\/gkq1091","volume":"39","author":"U Pieper","year":"2011","unstructured":"Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sj\u00f6lander K, Ferrin TE, Burley SK, Sali A: ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011, 39: D465-D474. 10.1093\/nar\/gkq1091.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR11","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4612-6137-7","volume-title":"Principles of Protein Structure","author":"GE Schulz","year":"1979","unstructured":"Schulz GE, Schirmer RH: Principles of Protein Structure. 1979, New York, NY, USA: Springer-Verlag"},{"key":"6341_CR12","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4899-1146-9","volume-title":"Molecular Biology of Membranes: Structure and Function","author":"HR Petty","year":"1993","unstructured":"Petty HR: Molecular Biology of Membranes: Structure and Function. 1993, New York, NY, USA: Plenum"},{"key":"6341_CR13","doi-asserted-by":"publisher","first-page":"e1000485","DOI":"10.1371\/journal.pcbi.1000485","volume":"5","author":"OC Redfern","year":"2009","unstructured":"Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA: FLORA: a novel method to predict protein function from structure in diverse superfamilies. PLoS Comput Biol. 2009, 5: e1000485-10.1371\/journal.pcbi.1000485.","journal-title":"PLoS Comput Biol"},{"key":"6341_CR14","doi-asserted-by":"crossref","first-page":"A296","DOI":"10.1096\/fj.07-0104ufm","volume":"21","author":"BR Hanson","year":"2007","unstructured":"Hanson BR, Westin C, Craig PA: Using PyMOL\u2019s selection algebra for enzyme catalytic site prediction. FASEB J. 2007, 21: A296-","journal-title":"FASEB J"},{"key":"6341_CR15","volume-title":"The PyMOL Molecular Graphics System","author":"WL Delano","year":"2002","unstructured":"Delano WL: The PyMOL Molecular Graphics System. 2002, San Carlos, CA, USA: Schrodinger, LLC"},{"key":"6341_CR16","doi-asserted-by":"publisher","first-page":"D129","DOI":"10.1093\/nar\/gkh028","volume":"32","author":"CT Porter","year":"2004","unstructured":"Porter CT: The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 2004, 32: D129-D133. 10.1093\/nar\/gkh028.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR17","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1002\/bmb.2006.494034062672","volume":"34","author":"L Grell","year":"2006","unstructured":"Grell L, Parkin C, Slatest L, Craig PA: EZ-Viz, a tool for simplifying molecular viewing in PyMOL. Biochem Mol Biol Educ. 2006, 34: 402-407. 10.1002\/bmb.2006.494034062672.","journal-title":"Biochem Mol Biol Educ"},{"key":"6341_CR18","first-page":"707","volume":"10","author":"VI Levenshtein","year":"1966","unstructured":"Levenshtein VI: Binary codes capable of correcting deletions, insertions, and reversals. Sov Phys-Dokl. 1966, 10: 707-710.","journal-title":"Sov Phys-Dokl"},{"key":"6341_CR19","volume-title":"TreeWidgets","author":"M Gushee","year":"2002","unstructured":"Gushee M: TreeWidgets. 2002, [http:\/\/matt.gushee.net\/software\/treewidgets\/]"},{"key":"6341_CR20","volume-title":"Remote PDB Loader","author":"C Moad","year":"2004","unstructured":"Moad C: Remote PDB Loader. 2004, [http:\/\/www.pymolwiki.org\/index.php\/Plugins_Tutorial]"},{"key":"6341_CR21","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1093\/bioinformatics\/btg226","volume":"19","author":"JA Barker","year":"2003","unstructured":"Barker JA, Thornton JM: An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics. 2003, 19: 1644-1649. 10.1093\/bioinformatics\/btg226.","journal-title":"Bioinformatics"},{"key":"6341_CR22","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1089\/cmb.1998.5.41","volume":"5","author":"V Escalier","year":"1998","unstructured":"Escalier V, Pothier J, Soldano H, Viari A: Pairwise and multiple identification of three-dimensional common substructures in proteins. J Comput Biol. 1998, 5: 41-56. 10.1089\/cmb.1998.5.41.","journal-title":"J Comput Biol"},{"key":"6341_CR23","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/S0097-8485(98)00017-5","volume":"22","author":"M Petitjean","year":"1998","unstructured":"Petitjean M: Interactive maximal common 3D substructure searching with the combined SDM\/RMS Algorithm. Comp Chem. 1998, 22: 463-465. 10.1016\/S0097-8485(98)00017-5.","journal-title":"Comp Chem"},{"key":"6341_CR24","doi-asserted-by":"publisher","first-page":"W549","DOI":"10.1093\/nar\/gkh439","volume":"32","author":"VA Ivanisenko","year":"2004","unstructured":"Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA: PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res. 2004, 32: W549-W554. 10.1093\/nar\/gkh439.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR25","doi-asserted-by":"publisher","first-page":"W459","DOI":"10.1093\/nar\/gkp304","volume":"37","author":"G Debret","year":"2009","unstructured":"Debret G, Martel A, Cuniasse P: RASMOT-3D PRO: a 3D motif search webserver. Nucleic Acids Res. 2009, 37: W459-W464. 10.1093\/nar\/gkp304.","journal-title":"Nucleic Acids Res"},{"key":"6341_CR26","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1186\/1471-2105-13-173","volume":"13","author":"MU Johansson","year":"2012","unstructured":"Johansson MU, Zoete V, Michielin O, Guex N: Defining and searching for structural motifs using DeepView\/Swiss-PdbViewer. BMC Bioinforma. 2012, 13: 173-10.1186\/1471-2105-13-173.","journal-title":"BMC Bioinforma"},{"key":"6341_CR27","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","volume":"7","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S\u00f6ding J, Thompson JD, Higgins DG: Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol. 2011, 7: 539-","journal-title":"Mol Syst Biol"},{"key":"6341_CR28","doi-asserted-by":"crossref","first-page":"811.1","DOI":"10.1096\/fasebj.27.1_supplement.811.1","volume":"27","author":"G Dodge","year":"2013","unstructured":"Dodge G, Arroyo EN, Bernstein HJ, Craig PA: Development and testing of a systematic approach for computational enzyme function determination. FASEB J. 2013, 27: 811.1-","journal-title":"FASEB J"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-87.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T03:29:26Z","timestamp":1630553366000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-87"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,27]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6341"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-87","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,3,27]]},"assertion":[{"value":"6 March 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"87"}}