{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T10:23:32Z","timestamp":1762251812865,"version":"3.40.1"},"reference-count":62,"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":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>This report describes the development and use of \"Cross Profile Analysis\" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Cross profile analysis reveals the polyphyletic and convergent evolution of \u03b2-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-13-11","type":"journal-article","created":{"date-parts":[[2012,1,17]],"date-time":"2012-01-17T07:26:52Z","timestamp":1326785212000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Convergent evolution in structural elements of proteins investigated using cross profile analysis"],"prefix":"10.1186","volume":"13","author":[{"given":"Kentaro","family":"Tomii","sequence":"first","affiliation":[]},{"given":"Yoshito","family":"Sawada","sequence":"additional","affiliation":[]},{"given":"Shinya","family":"Honda","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,1,16]]},"reference":[{"issue":"2-3","key":"5038_CR1","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1006\/jsbi.2001.4393","volume":"134","author":"AN Lupas","year":"2001","unstructured":"Lupas AN, Ponting CP, Russell RB: On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 2001, 134(2\u20133):191\u2013203. 10.1006\/jsbi.2001.4393","journal-title":"J Struct Biol"},{"issue":"13","key":"5038_CR2","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 USA 1987, 84(13):4355\u20134358. 10.1073\/pnas.84.13.4355","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"5038_CR3","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1002\/prot.20184","volume":"57","author":"T Ohlson","year":"2004","unstructured":"Ohlson T, Wallner B, Elofsson A: Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 2004, 57(1):188\u2013197. 10.1002\/prot.20184","journal-title":"Proteins"},{"issue":"2","key":"5038_CR4","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1110\/ps.9.2.232","volume":"9","author":"L Rychlewski","year":"2000","unstructured":"Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9(2):232\u2013241.","journal-title":"Protein Sci"},{"issue":"2","key":"5038_CR5","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1093\/nar\/gkg154","volume":"31","author":"AR Panchenko","year":"2003","unstructured":"Panchenko AR: Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res 2003, 31(2):683\u2013689. 10.1093\/nar\/gkg154","journal-title":"Nucleic Acids Res"},{"key":"5038_CR6","series-title":"Nucleic Acids Res","first-page":"W284","volume-title":"FFAS03: a server for profile-profile sequence alignments","author":"L Jaroszewski","year":"2005","unstructured":"Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A: FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 2005, (33 Web Server):W284\u2013288."},{"issue":"8","key":"5038_CR7","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1016\/j.str.2005.05.009","volume":"13","author":"I Friedberg","year":"2005","unstructured":"Friedberg I, Godzik A: Connecting the protein structure universe by using sparse recurring fragments. Structure 2005, 13(8):1213\u20131224. 10.1016\/j.str.2005.05.009","journal-title":"Structure"},{"issue":"3","key":"5038_CR8","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1016\/j.jmb.2005.08.071","volume":"354","author":"DL Theobald","year":"2005","unstructured":"Theobald DL, Wuttke DS: Divergent evolution within protein superfolds inferred from profile-based phylogenetics. J Mol Biol 2005, 354(3):722\u2013737. 10.1016\/j.jmb.2005.08.071","journal-title":"J Mol Biol"},{"issue":"14","key":"5038_CR9","doi-asserted-by":"publisher","first-page":"5441","DOI":"10.1073\/pnas.0704422105","volume":"105","author":"L Xie","year":"2008","unstructured":"Xie L, Bourne PE: Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci USA 2008, 105(14):5441\u20135446. 10.1073\/pnas.0704422105","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"5038_CR10","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1093\/molbev\/msq017","volume":"27","author":"M Remmert","year":"2010","unstructured":"Remmert M, Biegert A, Linke D, Lupas AN, Soding J: Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin. Mol Biol Evol 2010, 27(6):1348\u20131358. 10.1093\/molbev\/msq017","journal-title":"Mol Biol Evol"},{"issue":"3","key":"5038_CR11","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/j.sbi.2006.05.006","volume":"16","author":"RL Dunbrack Jr","year":"2006","unstructured":"Dunbrack RL Jr: Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006, 16(3):374\u2013384. 10.1016\/j.sbi.2006.05.006","journal-title":"Curr Opin Struct Biol"},{"issue":"2","key":"5038_CR12","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/protein\/2.2.77","volume":"2","author":"WR Taylor","year":"1988","unstructured":"Taylor WR: Pattern matching methods in protein sequence comparison and structure prediction. Protein Eng 1988, 2(2):77\u201386. 10.1093\/protein\/2.2.77","journal-title":"Protein Eng"},{"issue":"3","key":"5038_CR13","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 motifs. J Mol Biol 1998, 281(3):565\u2013577. 10.1006\/jmbi.1998.1943","journal-title":"J Mol Biol"},{"issue":"3","key":"5038_CR14","doi-asserted-by":"crossref","first-page":"381","DOI":"10.3233\/ISB-00141","volume":"4","author":"AG de Brevern","year":"2004","unstructured":"de Brevern AG, Benros C, Gautier R, Valadie H, Hazout S, Etchebest C: Local backbone structure prediction of proteins. In Silico Biol 2004, 4(3):381\u2013386.","journal-title":"In Silico Biol"},{"issue":"5","key":"5038_CR15","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1110\/ps.04956305","volume":"14","author":"K Ikeda","year":"2005","unstructured":"Ikeda K, Tomii K, Yokomizo T, Mitomo D, Maruyama K, Suzuki S, Higo J: Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci 2005, 14(5):1253\u20131265. 10.1110\/ps.04956305","journal-title":"Protein Sci"},{"issue":"4","key":"5038_CR16","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1529\/biophysj.105.076661","volume":"91","author":"Y Sawada","year":"2006","unstructured":"Sawada Y, Honda S: Structural diversity of protein segments follows a power-law distribution. Biophys J 2006, 91(4):1213\u20131223. 10.1529\/biophysj.105.076661","journal-title":"Biophys J"},{"issue":"2","key":"5038_CR17","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1002\/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M","volume":"27","author":"JS Fetrow","year":"1997","unstructured":"Fetrow JS, Palumbo MJ, Berg G: Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 1997, 27(2):249\u2013271. 10.1002\/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M","journal-title":"Proteins"},{"issue":"4","key":"5038_CR18","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1002\/1097-0134(20000901)40:4<662::AID-PROT90>3.0.CO;2-F","volume":"40","author":"C Micheletti","year":"2000","unstructured":"Micheletti C, Seno F, Maritan A: Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins 2000, 40(4):662\u2013674. 10.1002\/1097-0134(20000901)40:4<662::AID-PROT90>3.0.CO;2-F","journal-title":"Proteins"},{"issue":"12","key":"5038_CR19","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1093\/bioinformatics\/18.12.1650","volume":"18","author":"AS Yang","year":"2002","unstructured":"Yang AS, Wang LY: Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics 2002, 18(12):1650\u20131657. 10.1093\/bioinformatics\/18.12.1650","journal-title":"Bioinformatics"},{"issue":"4","key":"5038_CR20","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1002\/prot.20158","volume":"56","author":"J Pei","year":"2004","unstructured":"Pei J, Grishin NV: Combining evolutionary and structural information for local protein structure prediction. Proteins 2004, 56(4):782\u2013794. 10.1002\/prot.20158","journal-title":"Proteins"},{"issue":"4","key":"5038_CR21","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1093\/bioinformatics\/btg474","volume":"20","author":"K Tomii","year":"2004","unstructured":"Tomii K, Akiyama Y: FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics 2004, 20(4):594\u2013595. 10.1093\/bioinformatics\/btg474","journal-title":"Bioinformatics"},{"issue":"Suppl 7","key":"5038_CR22","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1002\/prot.20727","volume":"61","author":"K Tomii","year":"2005","unstructured":"Tomii K, Hirokawa T, Motono C: Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 2005, 61(Suppl 7):114\u2013121.","journal-title":"Proteins"},{"issue":"6","key":"5038_CR23","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 Data Bank? An update. Protein Eng 2003, 16(6):407\u2013414. 10.1093\/protein\/gzg052","journal-title":"Protein Eng"},{"issue":"9","key":"5038_CR24","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1002\/bies.10321","volume":"25","author":"J Soding","year":"2003","unstructured":"Soding J, Lupas AN: More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 2003, 25(9):837\u2013846. 10.1002\/bies.10321","journal-title":"Bioessays"},{"issue":"4","key":"5038_CR25","doi-asserted-by":"publisher","first-page":"1836","DOI":"10.1073\/pnas.042664399","volume":"99","author":"G Fritz","year":"2002","unstructured":"Fritz G, Roth A, Schiffer A, Buchert T, Bourenkov G, Bartunik HD, Huber H, Stetter KO, Kroneck PM, Ermler U: Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution. Proc Natl Acad Sci USA 2002, 99(4):1836\u20131841. 10.1073\/pnas.042664399","journal-title":"Proc Natl Acad Sci USA"},{"issue":"Pt 7","key":"5038_CR26","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1107\/S0907444902007333","volume":"58","author":"B Arnoux","year":"2002","unstructured":"Arnoux B, Ducruix A, Prange T: Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A). Acta Crystallogr D Biol Crystallogr 2002, 58(Pt 7):1252\u20131254.","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"4","key":"5038_CR27","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(4):536\u2013540.","journal-title":"J Mol Biol"},{"issue":"7","key":"5038_CR28","first-page":"703","volume":"2","author":"JH Hartwig","year":"1995","unstructured":"Hartwig JH: Actin-binding proteins. 1: Spectrin super family. Protein Profile 1995, 2(7):703\u2013800.","journal-title":"Protein Profile"},{"issue":"1","key":"5038_CR29","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/S0014-5793(01)03304-X","volume":"513","author":"K Djinovic-Carugo","year":"2002","unstructured":"Djinovic-Carugo K, Gautel M, Ylanne J, Young P: The spectrin repeat: a structural platform for cytoskeletal protein assemblies. FEBS Lett 2002, 513(1):119\u2013123. 10.1016\/S0014-5793(01)03304-X","journal-title":"FEBS Lett"},{"issue":"8","key":"5038_CR30","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","volume":"5","author":"CA Orengo","year":"1997","unstructured":"Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM: CATH--a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093\u20131108. 10.1016\/S0969-2126(97)00260-8","journal-title":"Structure"},{"doi-asserted-by":"crossref","unstructured":"Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al.: The Pfam protein families database. Nucleic Acids Res 2008, (38 Database):D211\u2013222.","key":"5038_CR31","DOI":"10.1093\/nar\/gkp985"},{"issue":"8","key":"5038_CR32","doi-asserted-by":"publisher","first-page":"1507","DOI":"10.1016\/j.str.2004.05.022","volume":"12","author":"S Honda","year":"2004","unstructured":"Honda S, Yamasaki K, Sawada Y, Morii H: 10 residue folded peptide designed by segment statistics. Structure 2004, 12(8):1507\u20131518. 10.1016\/j.str.2004.05.022","journal-title":"Structure"},{"issue":"3","key":"5038_CR33","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/S0959-440X(96)80058-3","volume":"6","author":"JF Gibrat","year":"1996","unstructured":"Gibrat JF, Madej T, Bryant SH: Surprising similarities in structure comparison. Curr Opin Struct Biol 1996, 6(3):377\u2013385. 10.1016\/S0959-440X(96)80058-3","journal-title":"Curr Opin Struct Biol"},{"key":"5038_CR34","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1039\/fd9949900245","volume":"99","author":"IB Grishina","year":"1994","unstructured":"Grishina IB, Woody RW: Contributions of tryptophan side chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators. Faraday Discuss 1994, (99):245\u2013262.","journal-title":"Faraday Discuss"},{"issue":"13","key":"5038_CR35","doi-asserted-by":"publisher","first-page":"4668","DOI":"10.1021\/ja043492e","volume":"127","author":"O Guvench","year":"2005","unstructured":"Guvench O, Brooks CL: Tryptophan side chain electrostatic interactions determine edge-to-face vs. parallel-displaced tryptophan side chain geometries in the designed beta-hairpin \"trpzip2\". J Am Chem Soc 2005, 127(13):4668\u20134674. 10.1021\/ja043492e","journal-title":"J Am Chem Soc"},{"issue":"46","key":"5038_CR36","doi-asserted-by":"publisher","first-page":"15327","DOI":"10.1021\/ja8030533","volume":"130","author":"S Honda","year":"2008","unstructured":"Honda S, Akiba T, Kato YS, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T, Harata K: Crystal structure of a ten-amino acid protein. J Am Chem Soc 2008, 130(46):15327\u201315331. 10.1021\/ja8030533","journal-title":"J Am Chem Soc"},{"issue":"3","key":"5038_CR37","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1021\/bi00779a019","volume":"10","author":"JE Brown","year":"1971","unstructured":"Brown JE, Klee WA: Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry 1971, 10(3):470\u2013476. 10.1021\/bi00779a019","journal-title":"Biochemistry"},{"issue":"5","key":"5038_CR38","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1021\/bi00056a004","volume":"32","author":"Y Kuroda","year":"1993","unstructured":"Kuroda Y: Residual helical structure in the C-terminal fragment of cytochrome c. Biochemistry 1993, 32(5):1219\u20131224. 10.1021\/bi00056a004","journal-title":"Biochemistry"},{"issue":"9","key":"5038_CR39","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1038\/nsb0994-584","volume":"1","author":"FJ Blanco","year":"1994","unstructured":"Blanco FJ, Rivas G, Serrano L: A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol 1994, 1(9):584\u2013590. 10.1038\/nsb0994-584","journal-title":"Nat Struct Biol"},{"issue":"2","key":"5038_CR40","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1006\/jmbi.1999.3346","volume":"295","author":"S Honda","year":"2000","unstructured":"Honda S, Kobayashi N, Munekata E: Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol 2000, 295(2):269\u2013278. 10.1006\/jmbi.1999.3346","journal-title":"J Mol Biol"},{"issue":"11","key":"5038_CR41","doi-asserted-by":"publisher","first-page":"2142","DOI":"10.1110\/ps.9.11.2142","volume":"9","author":"R Zerella","year":"2000","unstructured":"Zerella R, Chen PY, Evans PA, Raine A, Williams DH: Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding. Protein Sci 2000, 9(11):2142\u20132150. 10.1110\/ps.9.11.2142","journal-title":"Protein Sci"},{"issue":"6664","key":"5038_CR42","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1038\/34663","volume":"391","author":"A Crameri","year":"1998","unstructured":"Crameri A, Raillard SA, Bermudez E, Stemmer WP: DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 1998, 391(6664):288\u2013291. 10.1038\/34663","journal-title":"Nature"},{"issue":"3","key":"5038_CR43","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nbt0396-315","volume":"14","author":"A Crameri","year":"1996","unstructured":"Crameri A, Whitehorn EA, Tate E, Stemmer WP: Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol 1996, 14(3):315\u2013319. 10.1038\/nbt0396-315","journal-title":"Nat Biotechnol"},{"issue":"18","key":"5038_CR44","doi-asserted-by":"publisher","first-page":"10068","DOI":"10.1073\/pnas.170145497","volume":"97","author":"L Riechmann","year":"2000","unstructured":"Riechmann L, Winter G: Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc Natl Acad Sci USA 2000, 97(18):10068\u201310073.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"5038_CR45","doi-asserted-by":"publisher","first-page":"1880","DOI":"10.1073\/pnas.89.5.1880","volume":"89","author":"K Shiba","year":"1992","unstructured":"Shiba K, Schimmel P: Functional assembly of a randomly cleaved protein. Proc Natl Acad Sci USA 1992, 89(5):1880\u20131884. 10.1073\/pnas.89.5.1880","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"5038_CR46","doi-asserted-by":"publisher","first-page":"3805","DOI":"10.1073\/pnas.94.8.3805","volume":"94","author":"K Shiba","year":"1997","unstructured":"Shiba K, Takahashi Y, Noda T: Creation of libraries with long ORFs by polymerization of a microgene. Proc Natl Acad Sci USA 1997, 94(8):3805\u20133810. 10.1073\/pnas.94.8.3805","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"5038_CR47","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/protein\/12.8.673","volume":"12","author":"K Takahashi","year":"1999","unstructured":"Takahashi K, Noguti T, Hojo H, Yamauchi K, Kinoshita M, Aimoto S, Ohkubo T, Go M: A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. Protein Eng 1999, 12(8):673\u2013680. 10.1093\/protein\/12.8.673","journal-title":"Protein Eng"},{"issue":"8","key":"5038_CR48","doi-asserted-by":"crossref","first-page":"5861","DOI":"10.1016\/S0021-9258(18)53399-8","volume":"268","author":"H Yanagawa","year":"1993","unstructured":"Yanagawa H, Yoshida K, Torigoe C, Park JS, Sato K, Shirai T, Go M: Protein anatomy: functional roles of barnase module. J Biol Chem 1993, 268(8):5861\u20135865.","journal-title":"J Biol Chem"},{"issue":"12","key":"5038_CR49","doi-asserted-by":"publisher","first-page":"5814","DOI":"10.1073\/pnas.93.12.5814","volume":"93","author":"KF Han","year":"1996","unstructured":"Han KF, Baker D: Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci USA 1996, 93(12):5814\u20135818. 10.1073\/pnas.93.12.5814","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"5038_CR50","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1002\/pro.5560010313","volume":"1","author":"U Hobohm","year":"1992","unstructured":"Hobohm U, Scharf M, Schneider R, Sander C: Selection of representative protein data sets. Protein Sci 1992, 1(3):409\u2013417.","journal-title":"Protein Sci"},{"key":"5038_CR51","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-662-03978-6","volume-title":"Remote sensing digital image analysis","author":"JA Richards","year":"1999","unstructured":"Richards JA, Jia X: Remote sensing digital image analysis. New York: Springer; 1999."},{"issue":"3","key":"5038_CR52","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1007\/s10822-008-9248-x","volume":"23","author":"Y Sawada","year":"2009","unstructured":"Sawada Y, Honda S: ProSeg: a database of local structures of protein segments. J Comput Aided Mol Des 2009, 23(3):163\u2013169. 10.1007\/s10822-008-9248-x","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"5038_CR53","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1093\/nar\/30.1.260","volume":"30","author":"JM Chandonia","year":"2002","unstructured":"Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE: ASTRAL compendium enhancements. Nucleic Acids Res 2002, 30(1):260\u2013263. 10.1093\/nar\/30.1.260","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5038_CR54","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. Nucleic Acids Res 2000, 28(1):235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"key":"5038_CR55","series-title":"Nucleic Acids Res","first-page":"D13","volume-title":"Database resources of the National Center for Biotechnology Information","author":"DL Wheeler","year":"2008","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13\u201321."},{"issue":"13","key":"5038_CR56","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","volume":"22","author":"W Li","year":"2006","unstructured":"Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658\u20131659. 10.1093\/bioinformatics\/btl158","journal-title":"Bioinformatics"},{"issue":"2","key":"5038_CR57","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","volume":"292","author":"DT Jones","year":"1999","unstructured":"Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195\u2013202. 10.1006\/jmbi.1999.3091","journal-title":"J Mol Biol"},{"issue":"2","key":"5038_CR58","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1110\/ps.16802","volume":"11","author":"FM Pearl","year":"2002","unstructured":"Pearl FM, Lee D, Bray JE, Buchan DW, Shepherd AJ, Orengo CA: The CATH extended protein-family database: providing structural annotations for genome sequences. Protein Sci 2002, 11(2):233\u2013244.","journal-title":"Protein Sci"},{"issue":"12","key":"5038_CR59","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1093\/bioinformatics\/15.12.1000","volume":"15","author":"AA Schaffer","year":"1999","unstructured":"Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF: IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999, 15(12):1000\u20131011. 10.1093\/bioinformatics\/15.12.1000","journal-title":"Bioinformatics"},{"issue":"48","key":"5038_CR60","doi-asserted-by":"publisher","first-page":"50060","DOI":"10.1074\/jbc.M407837200","volume":"279","author":"K Shiozawa","year":"2004","unstructured":"Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H: Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. J Biol Chem 2004, 279(48):50060\u201350068. 10.1074\/jbc.M407837200","journal-title":"J Biol Chem"},{"key":"5038_CR61","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1471-2148-4-33","volume":"4","author":"W Cai","year":"2004","unstructured":"Cai W, Pei J, Grishin NV: Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol 2004, 4: 33. 10.1186\/1471-2148-4-33","journal-title":"BMC Evol Biol"},{"issue":"6","key":"5038_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(6):1188\u20131190. 10.1101\/gr.849004","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,18]],"date-time":"2025-03-18T22:09:06Z","timestamp":1742335746000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,16]]},"references-count":62,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5038"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2012,1,16]]},"assertion":[{"value":"20 June 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"11"}}