{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:49Z","timestamp":1740135169552,"version":"3.37.3"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,11,11]],"date-time":"2016-11-11T00:00:00Z","timestamp":1478822400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,11,11]],"date-time":"2016-11-11T00:00:00Z","timestamp":1478822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM60595","P41-GM103311"],"award-info":[{"award-number":["GM60595","P41-GM103311"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function determination is exceptionally time-consuming and can\u2019t keep pace with the identification of protein sequences. A tool, DASP (Deacon Active Site Profiler), was previously developed to identify protein sequences with active site similarity to a query set. Development of two iterative, automatable methods for clustering proteins into functionally relevant groups exposed algorithmic limitations to DASP.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The accuracy and efficiency of DASP was significantly improved through six algorithmic enhancements implemented in two stages: DASP2 and DASP3. Validation demonstrated DASP3 provides greater score separation between true positives and false positives than earlier versions. In addition, DASP3 shows similar performance to previous versions in clustering protein structures into isofunctional groups (validated against manual curation), but DASP3 gathers and clusters protein sequences into isofunctional groups more efficiently than DASP and DASP2.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>DASP algorithmic enhancements resulted in improved efficiency and accuracy of identifying proteins that contain active site features similar to those of the query set. These enhancements provide incremental improvement in structure database searches and initial sequence database searches; however, the enhancements show significant improvement in iterative sequence searches, suggesting DASP3 is an appropriate tool for the iterative processes required for clustering proteins into isofunctional groups.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1295-z","type":"journal-article","created":{"date-parts":[[2016,11,11]],"date-time":"2016-11-11T12:05:56Z","timestamp":1478865956000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["DASP3: identification of protein sequences belonging to functionally relevant groups"],"prefix":"10.1186","volume":"17","author":[{"given":"Janelle B.","family":"Leuthaeuser","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John H.","family":"Morris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela F.","family":"Harper","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas E.","family":"Ferrin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patricia C.","family":"Babbitt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacquelyn S.","family":"Fetrow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,11,11]]},"reference":[{"key":"1295_CR1","doi-asserted-by":"publisher","first-page":"D30","DOI":"10.1093\/nar\/gku1216","volume":"43","author":"DA Benson","year":"2015","unstructured":"Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2015;43:D30\u20135.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR2","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/0168-9525(96)60040-7","volume":"12","author":"P Bork","year":"1996","unstructured":"Bork P, Bairoch A. Go hunting in sequence databases but watch out for the traps. Trends Genet. 1996;12:425\u20137.","journal-title":"Trends Genet"},{"key":"1295_CR3","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1093\/bioinformatics\/14.9.753","volume":"14","author":"PD Karp","year":"1998","unstructured":"Karp PD. What we do not know about sequence analysis and sequence databases. Bioinformatics. 1998;14:753\u20134.","journal-title":"Bioinformatics"},{"key":"1295_CR4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1186\/1471-2105-9-353","volume":"9","author":"A Nagy","year":"2008","unstructured":"Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, B\u00e1nyai L, et al. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics. 2008;9:353.","journal-title":"BMC Bioinformatics"},{"key":"1295_CR5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000605","volume":"5","author":"AM Schnoes","year":"2009","unstructured":"Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol. 2009;5, e1000605.","journal-title":"PLoS Comput Biol"},{"key":"1295_CR6","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1002\/prot.24803","volume":"83","author":"GL Holliday","year":"2015","unstructured":"Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, et al. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015;83:1005\u201313.","journal-title":"Proteins"},{"key":"1295_CR7","doi-asserted-by":"publisher","first-page":"D521","DOI":"10.1093\/nar\/gkt1130","volume":"42","author":"E Akiva","year":"2014","unstructured":"Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, et al. The structure-function linkage database. Nucleic Acids Res. 2014;42:D521\u201330.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR8","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","volume":"42","author":"RD Finn","year":"2014","unstructured":"Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222\u201330.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR9","doi-asserted-by":"publisher","first-page":"D376","DOI":"10.1093\/nar\/gku947","volume":"43","author":"I Sillitoe","year":"2015","unstructured":"Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, et al. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 2015;43:D376\u201381.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR10","doi-asserted-by":"publisher","first-page":"D304","DOI":"10.1093\/nar\/gkt1240","volume":"42","author":"NK Fox","year":"2014","unstructured":"Fox NK, Brenner SE, Chandonia J-M. SCOPe: Structural Classification of Proteins\u2014extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014;42:D304\u20139.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR11","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1093\/nar\/gkp1049","volume":"38","author":"DA Lee","year":"2010","unstructured":"Lee DA, Rentzsch R, Orengo C. GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res. 2010;38:720\u201337.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030160","volume":"3","author":"DP Brown","year":"2007","unstructured":"Brown DP, Krishnamurthy N, Sj\u00f6lander K. Automated protein subfamily identification and classification. PLoS Comput Biol. 2007;3, e160.","journal-title":"PLoS Comput Biol"},{"key":"1295_CR13","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1016\/j.jmb.2006.04.055","volume":"360","author":"ME Glasner","year":"2006","unstructured":"Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, et al. Evolution of structure and function in the o-succinylbenzoate synthase\/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol. 2006;360:228\u201350.","journal-title":"J Mol Biol"},{"key":"1295_CR14","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1021\/bi802277h","volume":"48","author":"A Sakai","year":"2009","unstructured":"Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, et al. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in Two families of cis, cis-muconate lactonizing enzymes. Biochemistry (Mosc). 2009;48:1445\u201353.","journal-title":"Biochemistry (Mosc)"},{"key":"1295_CR15","doi-asserted-by":"publisher","first-page":"9944","DOI":"10.1021\/bi800914r","volume":"47","author":"JF Rakus","year":"2008","unstructured":"Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, et al. Evolution of enzymatic activities in the enolase superfamily: L-Rhamnonate dehydratase. Biochemistry (Mosc). 2008;47:9944\u201354.","journal-title":"Biochemistry (Mosc)"},{"key":"1295_CR16","doi-asserted-by":"publisher","first-page":"12896","DOI":"10.1021\/bi701703w","volume":"46","author":"JF Rakus","year":"2007","unstructured":"Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, et al. Evolution of enzymatic activities in the enolase superfamily: d-mannonate dehydratase from novosphingobium aromaticivorans. Biochemistry. 2007;46:12896\u2013908.","journal-title":"Biochemistry"},{"key":"1295_CR17","doi-asserted-by":"publisher","first-page":"14358","DOI":"10.1021\/bi981123n","volume":"37","author":"AM Gulick","year":"1998","unstructured":"Gulick AM, Palmer DRJ, Babbitt PC, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from pseudomonas putida. Biochemistry. 1998;37:14358\u201368.","journal-title":"Biochemistry"},{"key":"1295_CR18","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/j.jmb.2003.09.062","volume":"334","author":"S Cammer","year":"2003","unstructured":"Cammer S, Hoffman B, Speir J, Canady M, Nelson M, Knutson S, et al. Structure-based active site profiles for genome analysis and functional family subclassification. J Mol Biol. 2003;334:387\u2013401.","journal-title":"J Mol Biol"},{"key":"1295_CR19","first-page":"3590","volume":"22","author":"TK Attwood","year":"1994","unstructured":"Attwood TK, Beck ME, Bleasby AJ, Parry-Smith DJ. PRINTS--a database of protein motif fingerprints. Nucleic Acids Res. 1994;22:3590\u20136.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR20","doi-asserted-by":"publisher","first-page":"D213","DOI":"10.1093\/nar\/gku1243","volume":"43","author":"A Mitchell","year":"2015","unstructured":"Mitchell A, Chang H-Y, Daugherty L, Fraser M, Hunter S, Lopez R, et al. The InterPro protein families database: the classification resource after 15\u00a0years. Nucleic Acids Res. 2015;43:D213\u201321.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR21","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1093\/nar\/24.1.197","volume":"24","author":"S Pietrokovski","year":"1996","unstructured":"Pietrokovski S, Henikoff JG, Henikoff S. The blocks database\u2014a system for protein classification. Nucleic Acids Res. 1996;24:197\u2013200.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR22","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403\u201310.","journal-title":"J Mol Biol"},{"key":"1295_CR23","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S Altschul","year":"1997","unstructured":"Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389\u2013402.","journal-title":"Nucleic Acids Res"},{"key":"1295_CR24","volume-title":"DASP: Active Site Profiling for Identification of Functional Sites in Protein Sequences and Structures","author":"R Huff","year":"2005","unstructured":"Huff R. DASP: Active Site Profiling for Identification of Functional Sites in Protein Sequences and Structures. Winston-Salem: Wake Forest University; 2005."},{"key":"1295_CR25","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1002\/cbdv.200590125","volume":"2","author":"RG Huff","year":"2005","unstructured":"Huff RG, Bayram E, Tan H, Knutson ST, Knaggs MH, Richon AB, et al. Chemical and structural diversity in cyclooxygenase protein active sites. Chem Biodivers. 2005;2:1533\u201352.","journal-title":"Chem Biodivers"},{"key":"1295_CR26","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1002\/prot.22936","volume":"79","author":"KJ Nelson","year":"2011","unstructured":"Nelson KJ, Knutson ST, Soito L, Klomsiri C, Poole LB, Fetrow JS. Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis. Proteins. 2011;79:947\u201364.","journal-title":"Proteins"},{"key":"1295_CR27","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1002\/cbic.201500624","volume":"17","author":"JG Gober","year":"2016","unstructured":"Gober JG, Rydeen AE, Gibson-O\u2019Grady EJ, Leuthaeuser JB, Fetrow JS, Brustad EM. Mutating a highly conserved residue in diverse cytochrome P450s facilitates diastereoselective olefin cyclopropanation. Chembiochem Eur J Chem Biol. 2016;17:394\u20137.","journal-title":"Chembiochem Eur J Chem Biol"},{"key":"1295_CR28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0004345","volume":"4","author":"HJ Atkinson","year":"2009","unstructured":"Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE. 2009;4, e4345.","journal-title":"PLoS ONE"},{"key":"1295_CR29","doi-asserted-by":"publisher","first-page":"e1001843","DOI":"10.1371\/journal.pbio.1001843","volume":"12","author":"ST Mashiyama","year":"2014","unstructured":"Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, et al. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol. 2014;12:e1001843.","journal-title":"PLoS Biol"},{"key":"1295_CR30","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1002\/pro.2724","volume":"24","author":"JB Leuthaeuser","year":"2015","unstructured":"Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Sci Publ Protein Soc. 2015;24:1423\u201339.","journal-title":"Protein Sci Publ Protein Soc"},{"key":"1295_CR31","doi-asserted-by":"publisher","first-page":"4355","DOI":"10.1073\/pnas.84.13.4355","volume":"84","author":"M Gribskov","year":"1987","unstructured":"Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987;84:4355\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1295_CR32","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1093\/bioinformatics\/14.1.48","volume":"14","author":"TL Bailey","year":"1998","unstructured":"Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 1998;14:48\u201354.","journal-title":"Bioinformatics"},{"key":"1295_CR33","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1126\/science.1080405","volume":"300","author":"ZA Wood","year":"2003","unstructured":"Wood ZA, Poole LB, Karplus PA. Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling. Science. 2003;300:650\u20133.","journal-title":"Science"},{"key":"1295_CR34","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1016\/j.cbpa.2006.08.012","volume":"10","author":"ME Glasner","year":"2006","unstructured":"Glasner ME, Gerlt JA, Babbitt PC. Evolution of enzyme superfamilies. Curr Opin Chem Biol. 2006;10:492\u20137.","journal-title":"Curr Opin Chem Biol"},{"key":"1295_CR35","doi-asserted-by":"publisher","first-page":"4122","DOI":"10.1073\/pnas.1112081109","volume":"109","author":"T Lukk","year":"2012","unstructured":"Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, et al. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A. 2012;109:4122\u20137.","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1295-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1295-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1295-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:16:02Z","timestamp":1706811362000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1295-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,11]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1295"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1295-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2016,11,11]]},"assertion":[{"value":"22 April 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 October 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 November 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"458"}}