{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T20:03:23Z","timestamp":1777493003435,"version":"3.51.4"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/1471-2105-5-58","type":"journal-article","created":{"date-parts":[[2004,5,14]],"date-time":"2004-05-14T06:21:40Z","timestamp":1084515700000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Use of a structural alphabet for analysis of short loops connecting repetitive structures"],"prefix":"10.1186","volume":"5","author":[{"given":"Laurent","family":"Fourrier","sequence":"first","affiliation":[]},{"given":"Cristina","family":"Benros","sequence":"additional","affiliation":[]},{"given":"Alexandre G","family":"de Brevern","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,5,12]]},"reference":[{"key":"174_CR1","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1073\/pnas.37.5.235","volume":"37","author":"L Pauling","year":"1951","unstructured":"Pauling L, Corey RB: Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains.\n                           Proc Natl Acad Sci USA 1951, 37: 235\u2013240.","journal-title":"Proc Natl Acad Sci USA"},{"key":"174_CR2","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1073\/pnas.37.5.251","volume":"37","author":"L Pauling","year":"1951","unstructured":"Pauling L, Corey RB: The Pleated Sheet, A New Layer Configuration of Polypeptide Chains.\n                           Proc Natl Acad Sci USA 1951, 37: 251\u2013256.","journal-title":"Proc Natl Acad Sci USA"},{"key":"174_CR3","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.\n                           Biopolymers 1983, 22: 2577\u20132637.","journal-title":"Biopolymers"},{"key":"174_CR4","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.\n                           Proteins 1995, 23: 566\u2013579.","journal-title":"Proteins"},{"key":"174_CR5","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1002\/prot.340030202","volume":"3","author":"FM Ridchards","year":"1988","unstructured":"Ridchards FM, Kundrot CE: Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure.\n                           Proteins 1988, 3: 71\u201384.","journal-title":"Proteins"},{"key":"174_CR6","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1002\/prot.340060105","volume":"6","author":"H Sklenar","year":"1989","unstructured":"Sklenar H, Etchebest C, Lavery R: Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.\n                           Proteins 1989, 6: 46\u201360.","journal-title":"Proteins"},{"key":"174_CR7","first-page":"291","volume":"13","author":"G Labesse","year":"1997","unstructured":"Labesse G, Colloc'h N, Pothier J, Mornon J-P: P-SEA: a new efficient assignment of secondary structure from C\u03b1.\n                           Comput Appl Biosci 1997, 13: 291\u2013295.","journal-title":"Comput Appl Biosci"},{"key":"174_CR8","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1093\/protein\/6.4.377","volume":"6","author":"N Colloc'h","year":"1993","unstructured":"Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon J-P: Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment.\n                           Protein Eng 1993, 6: 377\u2013382.","journal-title":"Protein Eng"},{"key":"174_CR9","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1006\/jsbi.2001.4336","volume":"134","author":"B Rost","year":"2001","unstructured":"Rost B: Review: protein secondary structure prediction continues to rise.\n                           J Struct Biol 2001, 134: 204\u2013218. 10.1006\/jsbi.2001.4336","journal-title":"J Struct Biol"},{"key":"174_CR10","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1002\/prot.10082","volume":"47","author":"G Pollastri","year":"2002","unstructured":"Pollastri G, Przybylski D, Rost B, Baldi P: Improving the prediction of secondary structure in three and eight classes using recurrent neural networks and profiles.\n                           Proteins 2002, 47: 228\u2013235. 10.1002\/prot.10082","journal-title":"Proteins"},{"key":"174_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/abio.2000.4757","volume":"286","author":"KC Chou","year":"2000","unstructured":"Chou KC: Prediction of tight turns and their types in proteins.\n                           Anal Biochem 2000, 286: 1\u201316. 10.1006\/abio.2000.4757","journal-title":"Anal Biochem"},{"key":"174_CR12","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1006\/jmbi.1996.0819","volume":"266","author":"B Oliva","year":"1997","unstructured":"Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ: An automated classification of the structure of the protein loops.\n                           J Mol Biol 1997, 266: 814\u2013830. 10.1006\/jmbi.1996.0819","journal-title":"J Mol Biol"},{"key":"174_CR13","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1002\/(SICI)1097-0134(19980201)30:2<193::AID-PROT9>3.0.CO;2-O","volume":"30","author":"NS Boutonnet","year":"1998","unstructured":"Boutonnet NS, Kajava AV, Rooman MJ: Structural classification of alphabetabeta and betabetaalpha supersecondary structure.\n                           Proteins 1998, 30: 193\u2013212. 10.1002\/(SICI)1097-0134(19980201)30:2<193::AID-PROT9>3.3.CO;2-Q","journal-title":"Proteins"},{"key":"174_CR14","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1006\/jmbi.1999.2826","volume":"289","author":"J Wojick","year":"1999","unstructured":"Wojick J, Mornon J-P, Chomilier J: New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.\n                           J Mol Biol 1999, 289: 1469\u20131490. 10.1006\/jmbi.1999.2826","journal-title":"J Mol Biol"},{"key":"174_CR15","first-page":"319","volume-title":"In Recent Adv In Prot Eng","author":"AG de Brevern","year":"2001","unstructured":"de Brevern AG, Camproux A-C, Hazout S, Etchebest C, Tuffery P: Beyond the secondary structures: the structural alphabets.\n                           In Recent Adv In Prot Eng\n                           (Edited by: Sangadai SG). Trivandrum, India: Research Signpost 2001, 319\u2013331."},{"key":"174_CR16","volume-title":"PhD thesis. University of California, Computer Science Department","author":"R Karchin","year":"2003","unstructured":"Karchin R: Evaluating local structure alphabets for protein structure prediction.\n                           PhD thesis. University of California, Computer Science Department 2003."},{"key":"174_CR17","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/S0022-2836(02)00942-7","volume":"323","author":"R Kolodony","year":"2002","unstructured":"Kolodony R, Koehl P, Guibas L, Levitt M: Small libraries of protein fragments model native protein structures accurately.\n                           J Mol Biol 2002, 323: 297\u2013307. 10.1016\/S0022-2836(02)00942-7","journal-title":"J Mol Biol"},{"key":"174_CR18","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1006\/jmbi.1998.1943","volume":"281","author":"C Bystroff","year":"1998","unstructured":"Bystroff C, Baker D: Prediction of local structure in proteins using a library of sequence-structure motif.\n                           J Mol Biol 1998, 281: 565\u2013577. 10.1006\/jmbi.1998.1943","journal-title":"J Mol Biol"},{"key":"174_CR19","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1002\/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z","volume":"41","author":"AG de Brevern","year":"2000","unstructured":"de Brevern AG, Etchebest C, Hazout S: Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.\n                           Proteins 2000, 41: 271\u2013287. 10.1002\/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z","journal-title":"Proteins"},{"issue":"1\/2","key":"174_CR20","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1007\/s002140000227","volume":"106","author":"AG de Brevern","year":"2001","unstructured":"de Brevern AG, Hazout S: Compacting local protein folds by a \"Hybrid Protein Model\".\n                           Theor Chem Acc 2001, 106(1\/2):36\u201347.","journal-title":"Theor Chem Acc"},{"key":"174_CR21","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1093\/bioinformatics\/btf859","volume":"19","author":"AG de Brevern","year":"2003","unstructured":"de Brevern AG, Hazout S: 'Hybrid Protein Model' for optimally defining 3D protein structure fragments.\n                           Bioinformatics 2003, 19: 345\u2013353. 10.1093\/bioinformatics\/btf859","journal-title":"Bioinformatics"},{"key":"174_CR22","first-page":"53","volume":"1","author":"C Benros","year":"2003","unstructured":"Benros C, de Brevern AG, Hazout S: Hybrid Protein Model (HPM): A method for building a library of overlapping local structural prototypes. sensitivity study and improvements of the training.\n                           IEEE Int Work. NNSP 2003, 1: 53\u201370.","journal-title":"IEEE Int Work. NNSP"},{"key":"174_CR23","doi-asserted-by":"publisher","first-page":"2871","DOI":"10.1110\/ps.0220502","volume":"11","author":"AG de Brevern","year":"2002","unstructured":"de Brevern AG, Valadi\u00e9 H, Hazout S, Etchebest C: Extension of a local backbone description using a structural alphabet. A new approach to the sequence-structure relationship.\n                           Protein Sci 2002, 11: 2871\u20132886. 10.1110\/ps.0220502","journal-title":"Protein Sci"},{"key":"174_CR24","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1002\/prot.10369","volume":"51","author":"R Karchin","year":"2003","unstructured":"Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K: Hidden Markov models that use predicted local structure for fold recognition: alphabets of protein backbone geometry.\n                           Proteins 2003, 51: 504\u2013514. 10.1002\/prot.10369","journal-title":"Proteins"},{"key":"174_CR25","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1093\/protein\/5.7.629","volume":"5","author":"S Woodcock","year":"1992","unstructured":"Woodcock S, Mornon J-P, Henrissat B: Detection of secondary structure elements in proteins by hydrophobic cluster analysis.\n                           Prot Eng 1992, 5: 629\u2013635.","journal-title":"Prot Eng"},{"key":"174_CR26","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1002\/pro.5560070103","volume":"7","author":"R Aurora","year":"1998","unstructured":"Aurora R, Rose GD: Helix capping.\n                           Protein Sci 1998, 7: 21\u201338.","journal-title":"Protein Sci"},{"key":"174_CR27","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1214\/aoms\/1177729694","volume":"22","author":"S Kullback","year":"1951","unstructured":"Kullback S, Leibler RA: On information and sufficiency.\n                           Ann Math Stat 1951, 22: 79\u201386.","journal-title":"Ann Math Stat"},{"key":"174_CR28","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1002\/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4","volume":"34","author":"J Cuff","year":"1999","unstructured":"Cuff J, Barton G: Evaluation and Improvement of multiple sequence methods for protein secondary structure prediction.\n                           Proteins 1999, 34: 508\u2013519. 10.1002\/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4","journal-title":"Proteins"},{"key":"174_CR29","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1080\/07391102.2000.10506570","volume":"17","author":"M Bansal","year":"2000","unstructured":"Bansal M, Kumar S, Velavan R: HELANAL: a program to characterize helix geometry in proteins.\n                           J Bio Struct Dyn 2000, 17: 811\u2013820.","journal-title":"J Bio Struct Dyn"},{"key":"174_CR30","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1093\/protein\/15.5.353","volume":"15","author":"MN Fodje","year":"2002","unstructured":"Fodje MN, Al-Karadaghi S: Occurrence, conformational features and amino acid propensities for the pi-helix.\n                           Protein Eng 2002, 15: 353\u2013358. 10.1093\/protein\/15.5.353","journal-title":"Protein Eng"},{"key":"174_CR31","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1093\/protein\/gzg052","volume":"16","author":"P Du","year":"2003","unstructured":"Du P, Andrec M, Levy RM: Have we seen all structures corresponding to short protein fragments in the Protein Databank.\n                           Protein Eng 2003, 16: 407\u2013414. 10.1093\/protein\/gzg052","journal-title":"Protein Eng"},{"key":"174_CR32","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","volume":"9","author":"A Fiser","year":"2000","unstructured":"Fiser A, Do RK, Sali A: Modeling of loops in protein structures.\n                           Protein Sci 2000, 9: 1753\u20131773.","journal-title":"Protein Sci"},{"issue":"1\/2","key":"174_CR33","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1007\/s002140100261","volume":"106","author":"A-C Camproux","year":"2001","unstructured":"Camproux A-C, de Brevern AG, Hazout S, Tuffery P: Exploring the use of a structural alphabet for a structural prediction of protein loops.\n                           Theor Chem Acc 2001, 106(1\/2):28\u201335.","journal-title":"Theor Chem Acc"},{"key":"174_CR34","doi-asserted-by":"crossref","first-page":"53","DOI":"10.18388\/abp.2001_5111","volume":"48","author":"GV Nikiforovich","year":"2001","unstructured":"Nikiforovich GV, Galaktionov S, Balodis J, Marshall GR: Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the case of bacteriorhodopsin.\n                           Acta Biochimic Polonica 2001, 48: 53\u201364.","journal-title":"Acta Biochimic Polonica"},{"key":"174_CR35","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1002\/1097-0282(2001)60:2<153::AID-BIP1010>3.0.CO;2-6","volume":"60","author":"S Galaktionov","year":"2001","unstructured":"Galaktionov S, Nikiforovich GV, Marshall GR: Ab initio modeling of small, medium, and large loops in proteins.\n                           Biopolymers 2001, 60: 153\u2013168. 10.1002\/1097-0282(2001)60:2<153::AID-BIP1010>3.0.CO;2-6","journal-title":"Biopolymers"},{"key":"174_CR36","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0022-2836(03)00670-3","volume":"331","author":"JJ Gray","year":"2003","unstructured":"Gray JJ, Moghon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D: Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.\n                           J Mol Biol 2003, 331: 281\u2013299. 10.1016\/S0022-2836(03)00670-3","journal-title":"J Mol Biol"},{"key":"174_CR37","doi-asserted-by":"publisher","first-page":"1910","DOI":"10.1002\/jcc.10329","volume":"24","author":"K Bastard","year":"2003","unstructured":"Bastard K, Thureau A, Lavery R, Prevost C: Docking macromolecules with flexible segments.\n                           J Comp Chem 2003, 24: 1910\u20131920. 10.1002\/jcc.10329","journal-title":"J Comp Chem"},{"key":"174_CR38","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/BF00337288","volume":"43","author":"T Kohonen","year":"1982","unstructured":"Kohonen T: Self-organized formation of topologically correct feature maps.\n                           Biol Cybern 1982, 43: 59\u201369.","journal-title":"Biol Cybern"},{"key":"174_CR39","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1109\/5.18626","volume":"77","author":"LR Rabiner","year":"1989","unstructured":"Rabiner LR: A tutorial on Hidden Markov Models and selected applications in speech recognition.\n                           Proc of the IEEE 1989, 77: 257\u2013285. 10.1109\/5.18626","journal-title":"Proc of the IEEE"},{"key":"174_CR40","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/nar\/29.1.219","volume":"29","author":"T Noguchi","year":"2001","unstructured":"Noguchi T, Matsuda H, Akiyama Y: PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).\n                           Nucleic Acids Res 2001, 29: 219\u2013220. 10.1093\/nar\/29.1.219","journal-title":"Nucleic Acids Res"},{"key":"174_CR41","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 H, Shindyalov IN, Bourne PE: The Protein Data Bank.\n                           Nucl Acids Res 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucl Acids Res"},{"key":"174_CR42","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/S0263-7855(98)80030-1","volume":"6","author":"DJ Bacon","year":"1988","unstructured":"Bacon DJ, Anderson WF: A fast algorithm for rendering space filling molecules pictures.\n                           J Mol Graph 1988, 6: 219\u2013220. 10.1016\/S0263-7855(98)80030-1","journal-title":"J Mol Graph"},{"key":"174_CR43","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/S0076-6879(97)77028-9","volume":"277","author":"EA Merritt","year":"1997","unstructured":"Merritt EA, Bacon DJ: Raster3D: Photorealistic molecular graphics.\n                           Methods in Enzym 1997, 277: 505\u2013524. 10.1016\/S0076-6879(97)77028-9","journal-title":"Methods in Enzym"},{"key":"174_CR44","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1107\/S0021889891004399","volume":"24","author":"PJ Kraulis","year":"1991","unstructured":"Kraulis PJ: MOLSCRIPT: A Program to produce both detailed and schematic plots of protein structures.\n                           J Appl Cryst 1991, 24: 946\u2013950. 10.1107\/S0021889891004399","journal-title":"J Appl Cryst"},{"key":"174_CR45","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/0263-7855(96)00009-4","volume":"14","author":"R Koradi","year":"1996","unstructured":"Koradi R, Billeter M, Wuthrich K: MOLMOL: a program for display and analysis of macromolecular structures.\n                           J Mol Graph 1996, 14: 51\u201355. 10.1016\/0263-7855(96)00009-4","journal-title":"J Mol Graph"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T16:04:12Z","timestamp":1726243452000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-58"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,5,12]]},"references-count":45,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["174"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-58","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2004,5,12]]},"assertion":[{"value":"4 February 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"58"}}