{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:51:21Z","timestamp":1773273081372,"version":"3.50.1"},"reference-count":69,"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":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP\/GTP, NAD(P) and SAH\/SAM.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-247","type":"journal-article","created":{"date-parts":[[2011,6,21]],"date-time":"2011-06-21T06:20:21Z","timestamp":1308637221000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs"],"prefix":"10.1186","volume":"12","author":[{"given":"Leslie","family":"Regad","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliette","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne-Claude","family":"Camproux","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,6,20]]},"reference":[{"key":"4716_CR1","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2148-5-10","volume":"5","author":"AR Panchenko","year":"2005","unstructured":"Panchenko AR, Madej T: Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol Biol 2005, 5: 10. 10.1186\/1471-2148-5-10","journal-title":"BMC Evol Biol"},{"issue":"12","key":"4716_CR2","doi-asserted-by":"publisher","first-page":"2600","DOI":"10.1002\/pro.5560051223","volume":"5","author":"LE Donate","year":"1996","unstructured":"Donate LE, Rufino SD, Canard LH, Blundell TL: Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996, 5(12):2600\u20132616. 10.1002\/pro.5560051223","journal-title":"Protein Sci"},{"key":"4716_CR3","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 protein loops. J Mol Biol 1997, 266: 814\u2013830. 10.1006\/jmbi.1996.0819","journal-title":"J Mol Biol"},{"key":"4716_CR4","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1093\/bioinformatics\/16.6.513","volume":"16","author":"DF Burke","year":"2000","unstructured":"Burke DF, Deane CM, Blundell TL: Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. Bioinformatics 2000, 16: 513\u201319. 10.1093\/bioinformatics\/16.6.513","journal-title":"Bioinformatics"},{"key":"4716_CR5","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1006\/jmbi.1999.2826","volume":"289","author":"J Wojcik","year":"1999","unstructured":"Wojcik J, Mornon JP, Chomilier J: New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 1999, 289: 1469\u20131490. 10.1006\/jmbi.1999.2826","journal-title":"J Mol Biol"},{"issue":"3","key":"4716_CR6","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1002\/prot.20136","volume":"56","author":"N Fernandez-Fuentes","year":"2004","unstructured":"Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B: Classification of common functional loops of kinase super-families. Proteins 2004, 56(3):539\u2013555. 10.1002\/prot.20136","journal-title":"Proteins"},{"key":"4716_CR7","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1002\/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V","volume":"49","author":"W Li","year":"1999","unstructured":"Li W, Liu Z, Lai L: Protein loops on structurally similar scaffolds: database and conformational analysis. Biopolymers 1999, 49: 481. 10.1002\/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V","journal-title":"Biopolymers"},{"key":"4716_CR8","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1096\/fasebj.9.9.7601335","volume":"9","author":"JS Fetrow","year":"1995","unstructured":"Fetrow JS: Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J 1995, 9: 708\u2013717.","journal-title":"FASEB J"},{"key":"4716_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0014-5793(98)00606-1","volume":"430","author":"LN Johnson","year":"1998","unstructured":"Johnson LN, Lowe ED, Noble ME, Owen DJ: The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases. FEBS Lett 1998, 430: 1\u201311. 10.1016\/S0014-5793(98)00606-1","journal-title":"FEBS Lett"},{"key":"4716_CR10","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1016\/0968-0004(90)90281-F","volume":"15","author":"M Saraste","year":"1990","unstructured":"Saraste M, Sibbald PR, Wittinghofer A: The P-loop: a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 1990, 15: 430\u2013434. 10.1016\/0968-0004(90)90281-F","journal-title":"Trends Biochem Sci"},{"issue":"4","key":"4716_CR11","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1006\/jmbi.2000.4151","volume":"303","author":"A Via","year":"2000","unstructured":"Via A, Ferre F, Brannetti B, Valencia A, Helmer-Citterich M: Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. J Mol Biol 2000, 303(4):455\u2013465. 10.1006\/jmbi.2000.4151","journal-title":"J Mol Biol"},{"key":"4716_CR12","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1038\/324084a0","volume":"324","author":"D Stuart","year":"1986","unstructured":"Stuart D, Acharya K, Walker N, Smith S, Lewis M, Phillips D: Lactalbumin possesses a novel calcium binding loop. Nature 1986, 324: 84\u201387. 10.1038\/324084a0","journal-title":"Nature"},{"key":"4716_CR13","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1186\/1471-2105-9-312","volume":"9","author":"A Golovin","year":"2008","unstructured":"Golovin A, Henrick K: MSDmotif: exploring protein sites and motifs. BMC Bioinformatics 2008, 9: 312\u2013312. 10.1186\/1471-2105-9-312","journal-title":"BMC Bioinformatics"},{"key":"4716_CR14","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1093\/bioinformatics\/btl382","volume":"22","author":"J Espadaler","year":"2006","unstructured":"Espadaler J, Querol E, Aviles FX, Oliva B: Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics 2006, 22: 2237\u20132243. 10.1093\/bioinformatics\/btl382","journal-title":"Bioinformatics"},{"key":"4716_CR15","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1093\/nar\/gkm977","volume":"36","author":"N Hulo","year":"2007","unstructured":"Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche B, De Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJA: The 20 years of PROSITE. Nucleic Acids Res 2007, 36: 245\u2013249. 10.1093\/nar\/gkm1044","journal-title":"Nucleic Acids Res"},{"key":"4716_CR16","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"4716_CR17","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1016\/j.jmb.2004.02.047","volume":"338","author":"AV Tendulkar","year":"2004","unstructured":"Tendulkar AV, Joshi AA, Sohoni MA, Wangikar PP: Clustering of protein structural fragments reveals modular building block approach of nature. J Mol Biol 2004, 338: 611\u2013629. 10.1016\/j.jmb.2004.02.047","journal-title":"J Mol Biol"},{"issue":"3","key":"4716_CR18","doi-asserted-by":"publisher","first-page":"R52","DOI":"10.1186\/gb-2008-9-3-r52","volume":"9","author":"K Manikandan","year":"2008","unstructured":"Manikandan K, Pal D, Ramakumar S, Brener N, Iyengar S, Seetharaman G: Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. Genome Biol 2008, 9(3):R52. 10.1186\/gb-2008-9-3-r52","journal-title":"Genome Biol"},{"key":"4716_CR19","first-page":"536","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\u2013540.","journal-title":"J Mol Biol"},{"key":"4716_CR20","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1093\/bioinformatics\/btk038","volume":"22","author":"BJ Polacco","year":"2006","unstructured":"Polacco BJ, Babbitt PC: Automated discovery of 3D motifs for protein function annotation. Bioinformatics 2006, 22: 723\u2013730. 10.1093\/bioinformatics\/btk038","journal-title":"Bioinformatics"},{"key":"4716_CR21","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-9-S2-S2","volume":"9","author":"G Ausiello","year":"2008","unstructured":"Ausiello G, Gherardini P, Marcatili P, Tramontano A, Via A, Helmer-Citterich M: FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics 2008, 9: S2.","journal-title":"BMC Bioinformatics"},{"key":"4716_CR22","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.jmb.2004.07.019","volume":"342","author":"J Sodhi","year":"2004","unstructured":"Sodhi J, Bryson K, McGuffin L, Ward J, Wernisch L, Jones D: Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 2004, 342: 307\u2013320. 10.1016\/j.jmb.2004.07.019","journal-title":"J Mol Biol"},{"key":"4716_CR23","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1186\/1471-2105-8-321","volume":"8","author":"J Nebel","year":"2007","unstructured":"Nebel J, Herzyk P, Gilbert D: Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 2007, 8: 321\u2013321. 10.1186\/1471-2105-8-321","journal-title":"BMC Bioinformatics"},{"issue":"24","key":"4716_CR24","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btn543","volume":"24","author":"A Bordner","year":"2008","unstructured":"Bordner A: Predicting small ligand binding sites in proteins using backbone structure. Bioinformatics 2008, 24(24):2865\u20132871. 10.1093\/bioinformatics\/btn543","journal-title":"Bioinformatics"},{"key":"4716_CR25","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1110\/ps.073138508","volume":"17","author":"J Ebert","year":"2008","unstructured":"Ebert J, Altman R: Robust recognition of zinc binding sites in proteins. Protein Sci 2008, 17: 54\u201365.","journal-title":"Protein Sci"},{"key":"4716_CR26","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2164-9-S2-S2","volume":"9","author":"I Halperin","year":"2008","unstructured":"Halperin I, Glazer D, Wu S, Altman R: The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics 2008, 9: S2.","journal-title":"BMC Genomics"},{"key":"4716_CR27","doi-asserted-by":"publisher","first-page":"e1000105","DOI":"10.1371\/journal.pcbi.1000105","volume":"4","author":"N Weinhold","year":"2008","unstructured":"Weinhold N, Sander O, Domingues F, Lengauer T, Sommer I: Local function conservation in sequence and structure space. PLoS Comput Biol 2008, 4: e1000105. 10.1371\/journal.pcbi.1000105","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"4716_CR28","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/pro.5560040404","volume":"4","author":"S Bagley","year":"1995","unstructured":"Bagley S, Altman R: Characterizing the microenvironment surrounding protein sites. Protein Sci 1995, 4(4):622\u2013635.","journal-title":"Protein Sci"},{"key":"4716_CR29","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1089\/cmb.1996.3.345","volume":"3","author":"MY Leung","year":"1997","unstructured":"Leung MY, Marsh GM, Speed TP: Over- and underrepresentation of short DNA words in herpesvirus genomes. J Comput Biol 1997, 3: 345\u2013360.","journal-title":"J Comput Biol"},{"key":"4716_CR30","doi-asserted-by":"publisher","first-page":"2971","DOI":"10.1093\/nar\/26.12.2971","volume":"26","author":"E Rocha","year":"1998","unstructured":"Rocha E, Viari A, Danchin A: Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res 1998, 26: 2971\u20132980. 10.1093\/nar\/26.12.2971","journal-title":"Nucleic Acids Res"},{"key":"4716_CR31","doi-asserted-by":"publisher","first-page":"1363","DOI":"10.1093\/nar\/20.6.1363","volume":"20","author":"S Karlin","year":"1992","unstructured":"Karlin S, Burge C, Campbell AM: Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res 1992, 20: 1363\u20131370. 10.1093\/nar\/20.6.1363","journal-title":"Nucleic Acids Res"},{"key":"4716_CR32","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1046\/j.1365-2958.1998.00749.x","volume":"27","author":"S Sourice","year":"1998","unstructured":"Sourice S, Biaudet V, El Karoui M, Ehrlich S, Gruss A: Identification of the Chi site of Haemophilus influenzae as several sequences related to Escherichia coli Chi site. Mol Microbiol 1998, 27: 1021\u20131029. 10.1046\/j.1365-2958.1998.00749.x","journal-title":"Mol Microbiol"},{"key":"4716_CR33","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1093\/nar\/28.4.1000","volume":"28","author":"J van Helden","year":"2000","unstructured":"van Helden J, Olmo M, Perez-Ortin JE: Statistical analysis of yeast genomic downstream sequences revels putative polyadenylation signals. Nucleic Acids Res 2000, 28: 1000\u20131010. 10.1093\/nar\/28.4.1000","journal-title":"Nucleic Acids Res"},{"key":"4716_CR34","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1093\/protein\/12.12.1063","volume":"12","author":"AC Camproux","year":"1999","unstructured":"Camproux AC, Tuff\u00e9ry P, Chevrolat JP, Boisvieux J, Hazout S: Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng 1999, 12: 1063\u20131073. 10.1093\/protein\/12.12.1063","journal-title":"Protein Eng"},{"key":"4716_CR35","first-page":"33","volume":"101","author":"AC Camproux","year":"1999","unstructured":"Camproux AC, Tuff\u00e9ry P, Buffat L, Andr\u00e9 C, Boisvieux JF, Hazout S: Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model. TCA 1999, 101: 33\u201340.","journal-title":"TCA"},{"key":"4716_CR36","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.jmb.2004.04.005","volume":"339","author":"AC Camproux","year":"2004","unstructured":"Camproux AC, Gautier R, Tuff\u00e9ry T: A hidden Markov model derivated structural alphabet for proteins. J Mol Biol 2004, 339: 561\u2013605.","journal-title":"J Mol Biol"},{"key":"4716_CR37","first-page":"92","volume-title":"Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational, Toronto, September","author":"L Regad","year":"2006","unstructured":"Regad L, Martin J, Camproux AC: Identification of non Random Motifs in Loops Using a Structural Alphabet. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational, Toronto, September 2006, 92\u2013100."},{"key":"4716_CR38","doi-asserted-by":"publisher","first-page":"3051","DOI":"10.1093\/bioinformatics\/bti451","volume":"21","author":"G Nuel","year":"2005","unstructured":"Nuel G: S-SPatt: simple statistics for patterns on Markov chains. Bioinformatics 2005, 21: 3051\u20133052. 10.1093\/bioinformatics\/bti451","journal-title":"Bioinformatics"},{"key":"4716_CR39","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2105-11-75","volume":"11","author":"L Regad","year":"2010","unstructured":"Regad L, Martin J, Nuel G, Camproux AC: Mining protein loops using a structural alphabet and statistical exceptionality. BMC Bioinformatics 2010, 11: 75. 10.1186\/1471-2105-11-75","journal-title":"BMC Bioinformatics"},{"key":"4716_CR40","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","volume":"19","author":"G Wang","year":"2003","unstructured":"Wang G, Dunbrack R: PISCES: a protein sequence culling server. Bioinformatics 2003, 19: 1589\u20131591. 10.1093\/bioinformatics\/btg224","journal-title":"Bioinformatics"},{"key":"4716_CR41","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1093\/nar\/gki070","volume":"33","author":"A Bairoch","year":"2005","unstructured":"Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, 33: 154\u2013159.","journal-title":"Nucleic Acids Res"},{"issue":"23","key":"4716_CR42","doi-asserted-by":"publisher","first-page":"4297","DOI":"10.1093\/bioinformatics\/bti694","volume":"21","author":"A Martin","year":"2005","unstructured":"Martin A: Mapping PDB chains to UniProtKB entries. Bioinformatics 2005, 21(23):4297\u20134301. 10.1093\/bioinformatics\/bti694","journal-title":"Bioinformatics"},{"key":"4716_CR43","doi-asserted-by":"publisher","first-page":"26","DOI":"10.2202\/1544-6115.1219","volume":"5","author":"G Nuel","year":"2006","unstructured":"Nuel G: Numerical solutions for Patterns Statistics on Markov chains. Statistical Applications in Genetics and Molecular Biology 2006, 5: 26.","journal-title":"Statistical Applications in Genetics and Molecular Biology"},{"key":"4716_CR44","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1748-7188-5-15","volume":"5","author":"G Nuel","year":"2010","unstructured":"Nuel G, Regad L, Martin J, Camproux AC: Exact distribution of pattern in a set of random sequences generated by a Markov source: application to biological data. Algo Mol Biol 2010, 5: 15. 10.1186\/1748-7188-5-15","journal-title":"Algo Mol Biol"},{"key":"4716_CR45","doi-asserted-by":"crossref","unstructured":"Regad L, Martin J, Camproux A, Nuel G: Finite Markov chain embedding for the exact distribution of patterns in a set of random sequences 2007 chap. Advances in Data Analysis: Theory and Applications to Reliability and Inference, Data Mining, Bioinformatics, Lifetime Data and Neural Networks.171\u2013180.","DOI":"10.1007\/978-0-8176-4799-5_16"},{"key":"4716_CR46","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1002\/prot.20461","volume":"59","author":"P Fuchs","year":"2005","unstructured":"Fuchs P, Alix JF, Alain JP: High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins 2005, 59: 828\u2013839. 10.1002\/prot.20461","journal-title":"Proteins"},{"issue":"2","key":"4716_CR47","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1016\/0005-2795(73)90350-4","volume":"303","author":"PN Lewis","year":"1973","unstructured":"Lewis PN, Momany FA, Scheraga HA: Chain reversals in proteins. Biochim Biophys Acta 1973, 303(2):211\u2013229.","journal-title":"Biochim Biophys Acta"},{"key":"4716_CR48","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-10-60","volume":"10","author":"D Leader","year":"2009","unstructured":"Leader D, Milner-White E: Motivated proteins: a web application for studying small three-dimensional protein motifs. BMC Bioinformatics 2009, 10: 60\u201360. 10.1186\/1471-2105-10-60","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"4716_CR49","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1006\/jmbi.2001.5227","volume":"315","author":"J Watson","year":"2002","unstructured":"Watson J, Milner-White E: A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi, psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. J Mol Biol 2002, 315(2):171\u2013182. 10.1006\/jmbi.2001.5227","journal-title":"J Mol Biol"},{"issue":"4","key":"4716_CR50","doi-asserted-by":"publisher","first-page":"1076","DOI":"10.1016\/j.jmb.2008.11.007","volume":"385","author":"G Torrance","year":"2009","unstructured":"Torrance G, Leader D, Gilbert D, Milner-White E: A novel main chain motif in proteins bridged by cationic groups: the niche. J Mol Biol 2009, 385(4):1076\u20131086. 10.1016\/j.jmb.2008.11.007","journal-title":"J Mol Biol"},{"key":"4716_CR51","doi-asserted-by":"publisher","first-page":"W129","DOI":"10.1093\/nar\/gkh028","volume":"32","author":"C Porter","year":"2004","unstructured":"Porter C, Bartlett G, Thornton J: The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, 32: W129\u2013133.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"4716_CR52","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"A Wallace","year":"1995","unstructured":"Wallace A, Laskowski R, Thornton J: LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8(2):127\u2013134. 10.1093\/protein\/8.2.127","journal-title":"Protein Eng"},{"issue":"3","key":"4716_CR53","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1006\/jmbi.2000.3684","volume":"298","author":"M Andrade","year":"2000","unstructured":"Andrade M, Ponting C, Gibson T, Bork P: Homology-based method for identification of protein repeats using statistical significance estimates. J Mol Biol 2000, 298(3):521\u2013537. 10.1006\/jmbi.2000.3684","journal-title":"J Mol Biol"},{"key":"4716_CR54","first-page":"1425","volume-title":"Biopolymers","author":"CM Venkatachalam","year":"1968","unstructured":"Venkatachalam CM: Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968, 1425\u20131436."},{"key":"4716_CR55","doi-asserted-by":"publisher","first-page":"2207","DOI":"10.1002\/pro.5560031206","volume":"3","author":"E Hutchinson","year":"1994","unstructured":"Hutchinson E, Thornton J: A revised set of potentials for \u03b2 -turn formation in proteins. Protein Sci 1994, 3: 2207\u20132216. 10.1002\/pro.5560031206","journal-title":"Protein Sci"},{"key":"4716_CR56","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1002\/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V","volume":"38","author":"V Pavone","year":"1996","unstructured":"Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, Saviano M: Discovering protein secondary structures: classification and description of isolated \u03b1 -turns. Biopolymers 1996, 38: 705\u2013721. 10.1002\/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V","journal-title":"Biopolymers"},{"key":"4716_CR57","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1021\/ma60030a031","volume":"5","author":"BW Matthews","year":"1972","unstructured":"Matthews BW: The gamma turn. Evidence for a new folded conformation in proteins. Macromolecules 1972, 5: 818\u2013819. 10.1021\/ma60030a031","journal-title":"Macromolecules"},{"key":"4716_CR58","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1016\/0022-2836(88)90368-3","volume":"204","author":"EJ Milner-White","year":"1988","unstructured":"Milner-White EJ, Ross BM, Ismail R, Belhadj-Mostefa K, Poet R: One type of gamma-turn, rather than the other gives rise to chain reversal in proteins. J Mol Biol 1988, 204: 777\u2013782. 10.1016\/0022-2836(88)90368-3","journal-title":"J Mol Biol"},{"issue":"11","key":"4716_CR59","doi-asserted-by":"publisher","first-page":"2219","DOI":"10.1110\/ps.23101","volume":"10","author":"S Hayward","year":"2001","unstructured":"Hayward S: Peptide-plane flipping in proteins. Protein Sci 2001, 10(11):2219\u20132227.","journal-title":"Protein Sci"},{"issue":"3","key":"4716_CR60","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1002\/prot.20808","volume":"62","author":"J Lee","year":"2006","unstructured":"Lee J, Dubey V, Somasundaram T, Blaber M: Conversion of type I 4:6 to 3:5 beta-turn types in human acidic fibroblast growth factor: effects upon structure, stability, folding, and mitogenic function. Proteins 2006, 62(3):686\u2013697.","journal-title":"Proteins"},{"key":"4716_CR61","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/s11084-005-4582-7","volume":"35","author":"E Milner-White","year":"2005","unstructured":"Milner-White E, Russell M: Sites for phosphates and iron-sulfur thiolates in the first membranes: 3 to 6 residue anion-binding motifs (nests). Orig Life Evol Biosph 2005, 35: 19\u201327. 10.1007\/s11084-005-4582-7","journal-title":"Orig Life Evol Biosph"},{"key":"4716_CR62","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","volume":"14","author":"GE Crooks","year":"2004","unstructured":"Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: A sequence logo generator. Genome Res 2004, 14: 1188\u20131190. 10.1101\/gr.849004","journal-title":"Genome Res"},{"issue":"8","key":"4716_CR63","doi-asserted-by":"publisher","first-page":"2745","DOI":"10.1529\/biophysj.105.074401","volume":"90","author":"P Fuchs","year":"2006","unstructured":"Fuchs P, Bonvin A, Bochicchio B, Pepe A, Alix A, Tamburro A: Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophys J 2006, 90(8):2745\u20132759. 10.1529\/biophysj.105.074401","journal-title":"Biophys J"},{"issue":"23","key":"4716_CR64","doi-asserted-by":"publisher","first-page":"2771","DOI":"10.1007\/s00018-005-5187-z","volume":"62","author":"N Matsushima","year":"2005","unstructured":"Matsushima N, Tachi N, Kuroki Y, Enkhbayar P, Osaki M, Kamiya M, Kretsinger R: Structural analysis of leucine-rich-repeat variants in proteins associated with human diseases. Cell Mol Life Sci 2005, 62(23):2771\u20132791. 10.1007\/s00018-005-5187-z","journal-title":"Cell Mol Life Sci"},{"issue":"3","key":"4716_CR65","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1006\/jmbi.1998.1643","volume":"277","author":"A Kajava","year":"1998","unstructured":"Kajava A: Structural diversity of leucine-rich repeat proteins. J Mol Biol 1998, 277(3):519\u2013527. 10.1006\/jmbi.1998.1643","journal-title":"J Mol Biol"},{"key":"4716_CR66","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1016\/j.jmb.2004.08.077","volume":"343","author":"DJ Rigden","year":"2004","unstructured":"Rigden DJ, Galperin MY: The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution. J Mol Biol 2004, 343: 971\u2013984. 10.1016\/j.jmb.2004.08.077","journal-title":"J Mol Biol"},{"key":"4716_CR67","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1002\/prot.20431","volume":"59","author":"M Babor","year":"2005","unstructured":"Babor M, Greenblatt H, Edelman M, Sobolev V: Flexibility of metal binding sites in proteins on a database scale. Proteins 2005, 59: 221\u2013230. 10.1002\/prot.20431","journal-title":"Proteins"},{"key":"4716_CR68","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1093\/bioinformatics\/btl685","volume":"23","author":"A Sacan","year":"2007","unstructured":"Sacan A, Ozturk O, Ferhatosmanoglu H, Wang Y: LFM-Pro: a tool for detecting significant local structural sites in proteins. Bioinformatics 2007, 23: 709\u2013716. 10.1093\/bioinformatics\/btl685","journal-title":"Bioinformatics"},{"key":"4716_CR69","doi-asserted-by":"publisher","first-page":"e150","DOI":"10.1093\/nar\/gkq478","volume":"38","author":"C Wu","year":"2010","unstructured":"Wu C, Chen Y, Lim C: A structural-alphabet-based strategy for finding structural motifs across protein families. Nucleic Acids Res 2010, 38: e150. 10.1093\/nar\/gkq478","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-247.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T15:26:29Z","timestamp":1630509989000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-247"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,20]]},"references-count":69,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4716"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-247","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,6,20]]},"assertion":[{"value":"7 October 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 June 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 June 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"247"}}