{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,16]],"date-time":"2023-04-16T17:49:32Z","timestamp":1681667372012},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,7,3]],"date-time":"2007-07-03T00:00:00Z","timestamp":1183420800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-237","type":"journal-article","created":{"date-parts":[[2007,7,3]],"date-time":"2007-07-03T18:13:34Z","timestamp":1183486414000},"source":"Crossref","is-referenced-by-count":18,"title":["A topological algorithm for identification of structural domains of proteins"],"prefix":"10.1186","volume":"8","author":[{"given":"Frank","family":"Emmert-Streib","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arcady","family":"Mushegian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,7,3]]},"reference":[{"issue":"5759","key":"1609_CR1","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1126\/science.1121018","volume":"311","author":"JM Chandonia","year":"2006","unstructured":"Chandonia JM, Brenner SE: The Impact of Structural Genomics: Expectations and Outcomes. Science. 2006, 311 (5759): 347-351. 10.1126\/science.1121018.","journal-title":"Science"},{"key":"1609_CR2","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/scientificamerican1166-78","volume":"215","author":"DC Phillips","year":"1966","unstructured":"Phillips DC: The three-dimensional structure of an enzyme molecule. Sci Am. 1966, 215: 78-90.","journal-title":"Sci Am"},{"key":"1609_CR3","doi-asserted-by":"publisher","first-page":"D226","DOI":"10.1093\/nar\/gkh039","volume":"32","author":"A Andreeva","year":"2004","unstructured":"Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004, 32: D226-229. 10.1093\/nar\/gkh039.","journal-title":"Nucleic Acids Res"},{"key":"1609_CR4","doi-asserted-by":"publisher","first-page":"D201","DOI":"10.1093\/nar\/gki106","volume":"33","author":"NJea Mulder","year":"2005","unstructured":"Mulder NJea: InterPro, progress and status in 2005. Nucleic Acids Res. 2005, 33: D201-205. 10.1093\/nar\/gki106.","journal-title":"Nucleic Acids Res"},{"key":"1609_CR5","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1073\/pnas.70.3.697","volume":"70","author":"D Wetlaufer","year":"1973","unstructured":"Wetlaufer D: Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci. 1973, 70: 697-701. 10.1073\/pnas.70.3.697.","journal-title":"Proc Natl Acad Sci"},{"key":"1609_CR6","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/0022-2836(74)90136-3","volume":"85","author":"MG Rossmann","year":"1974","unstructured":"Rossmann MG, Liljas A: Recognition of structural domains in globular proteins. J Mol Biol. 1974, 85: 177-181. 10.1016\/0022-2836(74)90136-3.","journal-title":"J Mol Biol"},{"key":"1609_CR7","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1146\/annurev.bi.64.070195.001443","volume":"64","author":"RF Doolittle","year":"1995","unstructured":"Doolittle RF: The multiplicity of domains in proteins. Annu Rev Biochem. 1995, 64: 287-314. 10.1146\/annurev.bi.64.070195.001443.","journal-title":"Annu Rev Biochem"},{"key":"1609_CR8","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1016\/j.jmb.2004.03.053","volume":"339","author":"S Veretnik","year":"2004","unstructured":"Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN: Toward consistent assignment of structural domains in proteins. J Mol Biol. 2004, 339: 647-678. 10.1016\/j.jmb.2004.03.053.","journal-title":"J Mol Biol"},{"issue":"7","key":"1609_CR9","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"E AJ","year":"2002","unstructured":"AJ E, S VD, CA O: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30 (7): 1575-84. 10.1093\/nar\/30.7.1575.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1609_CR10","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1006\/jmbi.2001.5387","volume":"316","author":"G RA","year":"2002","unstructured":"RA G, J H: SnapDRAGON: a method to delineate protein structural domains from sequence data. J Mol Biol. 2002, 316 (3): 839-51. 10.1006\/jmbi.2001.5387.","journal-title":"J Mol Biol"},{"issue":"10","key":"1609_CR11","doi-asserted-by":"publisher","first-page":"2264","DOI":"10.1093\/bioinformatics\/bti363","volume":"21","author":"B K","year":"2005","unstructured":"K B, BK M, CG E: Prediction of protein interdomain linker regions by a hidden Markov model. Bioinformatics. 2005, 21 (10): 2264-70. 10.1093\/bioinformatics\/bti363.","journal-title":"Bioinformatics"},{"key":"1609_CR12","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1006\/jmbi.1995.0159","volume":"247","author":"AG Murzin","year":"1995","unstructured":"Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995, 247: 536-540. 10.1006\/jmbi.1995.0159.","journal-title":"J Mol Biol"},{"issue":"8","key":"1609_CR13","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","volume":"5","author":"C Orengo","year":"1997","unstructured":"Orengo C, Michie A, Jones S, Jones D, Swindells M, Thornton J: CATH-A Hierarchic Classification of Protein Domain Structures. Structure. 1997, 5 (8): 1093-1108. 10.1016\/S0969-2126(97)00260-8.","journal-title":"Structure"},{"key":"1609_CR14","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1016\/j.jmb.2006.05.060","volume":"361","author":"TA Holland","year":"2006","unstructured":"Holland TA, Veretnik S, Shindyalov IN, Bourne PE: Partitioning protein structures into domains: why is it so difficult?. J Mol Biol. 2006, 361: 562-590. 10.1016\/j.jmb.2006.05.060.","journal-title":"J Mol Biol"},{"issue":"3","key":"1609_CR15","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1093\/protein\/12.3.203","volume":"12","author":"WR Taylor","year":"1999","unstructured":"Taylor WR: Protein structural domain identification. Protein Eng. 1999, 12 (3): 203-216. 10.1093\/protein\/12.3.203.","journal-title":"Protein Eng"},{"key":"1609_CR16","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1017\/S0305004100027419","volume":"48","author":"RB Potts","year":"1953","unstructured":"Potts RB: Some generalized order-disorder transformations. Proceedings of the Cambridge Society. 1953, 48: 106-109.","journal-title":"Proceedings of the Cambridge Society"},{"key":"1609_CR17","doi-asserted-by":"publisher","first-page":"3251","DOI":"10.1103\/PhysRevLett.76.3251","volume":"76","author":"M Blatt","year":"1996","unstructured":"Blatt M, Wiesman S, Domany E: Superparamagnetic Clustering of Data. Phys Rev Lett. 1996, 76: 3251-10.1103\/PhysRevLett.76.3251.","journal-title":"Phys Rev Lett"},{"key":"1609_CR18","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1162\/neco.1997.9.8.1805","volume":"9","author":"M Blatt","year":"1997","unstructured":"Blatt M, Wiesman S, Domany E: Data Clustering using a model granular magnet. Neural Computation. 1997, 9: 1805-1842. 10.1162\/neco.1997.9.8.1805.","journal-title":"Neural Computation"},{"issue":"12","key":"1609_CR19","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1093\/bioinformatics\/16.12.1091","volume":"16","author":"Y Xu","year":"2000","unstructured":"Xu Y, Xu D, Gabow HN: Protein domain decomposition using a graph-theoretic approach. Bioinformatics. 2000, 16 (12): 1091-1104. 10.1093\/bioinformatics\/16.12.1091.","journal-title":"Bioinformatics"},{"issue":"3","key":"1609_CR20","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1093\/nar\/gkg189","volume":"31","author":"Jt Guo","year":"2003","unstructured":"Guo Jt, Xu D, D K, Xu Y: Improving the performance of DomainParser for structural domain partition using neural network. Nucl Acids Res. 2003, 31 (3): 944-952. 10.1093\/nar\/gkg189.","journal-title":"Nucl Acids Res"},{"key":"1609_CR21","volume-title":"Flows in Networks","author":"LR Ford","year":"1962","unstructured":"Ford LR, Fulkerson DR: Flows in Networks. 1962, Princeton University Press"},{"key":"1609_CR22","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1093\/nar\/gkh034","volume":"32","author":"JMG Chandonia","year":"2004","unstructured":"Chandonia JMG, Hon G, Lo Conte NS, Koehl P, Levitt M, Brenner SE: The ASTRAL compendium in 2004. Nucleic Acids Research. 2004, 32: 189-192. 10.1093\/nar\/gkh034.","journal-title":"Nucleic Acids Research"},{"key":"1609_CR23","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, Springer Publisher"},{"key":"1609_CR24","volume-title":"Proceedings of the tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","author":"T Horvath","year":"2004","unstructured":"Horvath T, G\u00e4rtner T, Wrobel S: Cyclic Pattern Kernels for Predictive Graph Mining. Proceedings of the tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 2004"},{"key":"1609_CR25","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1002\/pro.5560070202","volume":"7","author":"S Jones","year":"1998","unstructured":"Jones S, Steward M, Michie A, Swindells MB, Orengo C, Thornton JM: Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci. 1998, 7: 233-242.","journal-title":"Protein Sci"},{"issue":"15","key":"1609_CR26","doi-asserted-by":"publisher","first-page":"5964","DOI":"10.1063\/1.471328","volume":"104","author":"SJ Chen","year":"1996","unstructured":"Chen SJ, Dill KA: Symmetries in proteins: A knot theory approach. J Chem Phys. 1996, 104 (15): 5964-5973. 10.1063\/1.471328.","journal-title":"J Chem Phys"},{"issue":"6","key":"1609_CR27","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1089\/cmb.2005.12.609","volume":"12","author":"MA Erdmann","year":"2005","unstructured":"Erdmann MA: Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings. Journal of Computational Biology. 2005, 12 (6): 609-637. 10.1089\/cmb.2005.12.609.","journal-title":"Journal of Computational Biology"},{"key":"1609_CR28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1073\/pnas.2636460100","volume":"100","author":"P Rogen","year":"2003","unstructured":"Rogen P, Fain B: Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci USA. 2003, 100: 119-124. 10.1073\/pnas.2636460100.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"1609_CR29","doi-asserted-by":"publisher","first-page":"1503","DOI":"10.1089\/cmb.2006.13.1503","volume":"13","author":"F Emmert-Streib","year":"2006","unstructured":"Emmert-Streib F: Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins. Journal of Computational Biology. 2006, 13 (8): 1503-1512. 10.1089\/cmb.2006.13.1503.","journal-title":"Journal of Computational Biology"},{"key":"1609_CR30","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig , Shindyalov HIN, Bourne PE: The Protein Data Bank. Nucleic Acids Research. 2000, 28: 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucleic Acids Research"},{"key":"1609_CR31","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 1983, 22: 2577-2637. 10.1002\/bip.360221211.","journal-title":"Biopolymers"},{"key":"1609_CR32","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1002\/prot.340230412","volume":"23","author":"D Frishman","year":"1995","unstructured":"Frishman D, Argos P: Knowledge-based protein secondary structure assignment. Proteins. 1995, 23: 566-579. 10.1002\/prot.340230412.","journal-title":"Proteins"},{"issue":"3","key":"1609_CR33","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/0022-2836(79)90363-2","volume":"134","author":"GD Rose","year":"1979","unstructured":"Rose GD: Hierarchic organization of domains in globular proteins. J Mol Biol. 1979, 134 (3): 447-470. 10.1016\/0022-2836(79)90363-2.","journal-title":"J Mol Biol"},{"key":"1609_CR34","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1002\/pro.5560040507","volume":"4","author":"AS Siddiqui","year":"1995","unstructured":"Siddiqui AS, Barton GJ: Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions. Protein Science. 1995, 4: 872-884.","journal-title":"Protein Science"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-237.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-237\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-237.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T09:52:43Z","timestamp":1548237163000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-237"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,3]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1609"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-237","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,7,3]]},"article-number":"237"}}