{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,19]],"date-time":"2024-01-19T09:24:03Z","timestamp":1705656243602},"reference-count":41,"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":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order has also been used to select for viable protein folds from <jats:italic>ab initio<\/jats:italic> protein structure prediction programs. For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper, we propose several simple yet very effective methods to predict contact order from the amino acid sequence only. One set of methods is based on a weighted linear combination of predicted secondary structure content and amino acid composition. Depending on the number of components used in these equations it is possible to achieve a correlation coefficient of 0.857\u20130.870 between the observed and predicted contact order. A second method, based on sequence similarity to known three-dimensional structures, is able to achieve a correlation coefficient of 0.977. We have also developed a much more robust implementation for calculating contact order directly from PDB coordinates that works for &gt; 99% PDB files. All of these contact order predictors and calculators have been implemented as a web server (see Availability and requirements section for URL).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Protein contact order can be effectively predicted from the primary sequence, at the absence of three-dimensional structure. Three factors, percentage of residues in alpha helices, percentage of residues in beta strands, and sequence length, appear to be strongly correlated with the absolute contact order.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-255","type":"journal-article","created":{"date-parts":[[2008,5,31]],"date-time":"2008-05-31T06:13:20Z","timestamp":1212214400000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Protein contact order prediction from primary sequences"],"prefix":"10.1186","volume":"9","author":[{"given":"Yi","family":"Shi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianjun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Arndt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David S","family":"Wishart","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guohui","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,5,30]]},"reference":[{"key":"2240_CR1","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1146\/annurev.bi.59.070190.003215","volume":"59","author":"PS Kim","year":"1990","unstructured":"Kim PS, Baldwin RL: Intermediates in the folding reactions of small proteins. Annual Review of Biochemistry 1990, 59: 631\u2013660. 10.1146\/annurev.bi.59.070190.003215","journal-title":"Annual Review of Biochemistry"},{"key":"2240_CR2","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.sbi.2004.01.013","volume":"14","author":"J Kubelka","year":"2004","unstructured":"Kubelka J, Hofrichter J, Eaton WA: The protein folding \"speed limit\". Curr Opin Struct Biol 2004, 14: 76\u201388. 10.1016\/j.sbi.2004.01.013","journal-title":"Curr Opin Struct Biol"},{"key":"2240_CR3","doi-asserted-by":"publisher","first-page":"3802","DOI":"10.1073\/pnas.72.10.3802","volume":"72","author":"S Tanaka","year":"1975","unstructured":"Tanaka S, Scheraga HA: Model of protein folding: inclusion of short-, medium-, and long-range interactions. Proc Natl Acad Sci U S A 1975, 72: 3802\u20133806. 10.1073\/pnas.72.10.3802","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2240_CR4","doi-asserted-by":"publisher","first-page":"2796","DOI":"10.1021\/bi9823838","volume":"38","author":"Y Fezoui","year":"1999","unstructured":"Fezoui Y, Braswell EH, Xian W, Osterhout JJ: Dissection of the de novo designed peptide alpha-t-alpha: stability and properties of the intact molecule and its constituent helices. Biochemistry 1999, 38: 2796\u20132804. 10.1021\/bi9823838","journal-title":"Biochemistry"},{"key":"2240_CR5","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\u20132637. 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"key":"2240_CR6","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1006\/jmbi.1998.1645","volume":"277","author":"KW Plaxco","year":"1998","unstructured":"Plaxco KW, Simons KT, Baker D: Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998, 277: 985\u2013994. 10.1006\/jmbi.1998.1645","journal-title":"J Mol Biol"},{"key":"2240_CR7","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","volume":"55","author":"B Lee","year":"1971","unstructured":"Lee B, Richards FM: The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology 1971, 55: 379\u2013380. 10.1016\/0022-2836(71)90324-X","journal-title":"Journal of Molecular Biology"},{"key":"2240_CR8","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/S0959-440X(99)80027-X","volume":"9","author":"E Alm","year":"1999","unstructured":"Alm E, Baker D: Matching theory and experiment in protein folding. Current Opinion in Structural Biology 1999, 9: 189\u2013196. 10.1016\/S0959-440X(99)80027-X","journal-title":"Current Opinion in Structural Biology"},{"key":"2240_CR9","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/S0959-440X(00)00176-7","volume":"11","author":"V Grantcharova","year":"2001","unstructured":"Grantcharova V, Alm EJ, Baker D, Horwich AL: Mechanisms of protein folding. Current Opinion in Structural Biology 2001, 11: 70\u201382. 10.1016\/S0959-440X(00)00176-7","journal-title":"Current Opinion in Structural Biology"},{"key":"2240_CR10","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1110\/ps.3790102","volume":"11","author":"R Bonneau","year":"2002","unstructured":"Bonneau R, Ruczinski I, Tsai J, Baker D: Contact order and ab initio protein structure prediction. Protein Science 2002, 11: 1937\u20131944. 10.1110\/ps.3790102","journal-title":"Protein Science"},{"key":"2240_CR11","doi-asserted-by":"publisher","first-page":"2057","DOI":"10.1110\/ps.0302503","volume":"12","author":"DN Ivankov","year":"2003","unstructured":"Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV: Contact order revisited: Influence of protein size on the folding rate. Protein Sci 2003, 12: 2057\u20132062. 10.1110\/ps.0302503","journal-title":"Protein Sci"},{"key":"2240_CR12","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/35011000","volume":"405","author":"D Baker","year":"2000","unstructured":"Baker D: A surprising simplicity to protein folding. Nature 2000, 405: 39\u201342. 10.1038\/35011000","journal-title":"Nature"},{"key":"2240_CR13","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1006\/jmbi.2001.5037","volume":"313","author":"N Koga","year":"2001","unstructured":"Koga N, Takada S: Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. Journal of Molecular Biology 2001, 313: 171\u2013180. 10.1006\/jmbi.2001.5037","journal-title":"Journal of Molecular Biology"},{"key":"2240_CR14","doi-asserted-by":"publisher","first-page":"8942","DOI":"10.1073\/pnas.0402659101","volume":"101","author":"DN Ivankov","year":"2004","unstructured":"Ivankov DN, Finkelstein AV: Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proceedings of the National Academy of Sciences of the USA 2004, 101: 8942\u20138944. 10.1073\/pnas.0402659101","journal-title":"Proceedings of the National Academy of Sciences of the USA"},{"key":"2240_CR15","doi-asserted-by":"publisher","first-page":"W70","DOI":"10.1093\/nar\/gkl043","volume":"34","author":"MM Gromiha","year":"2006","unstructured":"Gromiha MM, Thangakani AM, Selvaraj S: FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Research 2006, 34: W70-W74. 10.1093\/nar\/gkl043","journal-title":"Nucleic Acids Research"},{"key":"2240_CR16","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1006\/jmbi.2001.4775","volume":"310","author":"MM Gromiha","year":"2001","unstructured":"Gromiha MM, Selvaraj S: Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. Journal of Molecular Biology 2001, 310: 27\u201332. 10.1006\/jmbi.2001.4775","journal-title":"Journal of Molecular Biology"},{"key":"2240_CR17","volume-title":"Website","author":"D Chivian","year":"2005","unstructured":"Chivian D, Kim DE, Malmstrom L, Schonbrun J, Rohl CA, Baker D: Prediction of CASP6 structures using automated Robetta protocols. Website 2005. [http:\/\/robetta.bakerlab.org\/pub\/dylan\/]"},{"key":"2240_CR18","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1186\/1471-2105-6-248","volume":"6","author":"Z Yuan","year":"2005","unstructured":"Yuan Z: Better prediction of protein contact number using a support vector regression analysis of amino acid sequence. BMC Bioinformatics 2005, 6: 248. 10.1186\/1471-2105-6-248","journal-title":"BMC Bioinformatics"},{"key":"2240_CR19","doi-asserted-by":"publisher","first-page":"67","DOI":"10.2142\/biophysics.1.67","volume":"1","author":"AR Kinjo","year":"2005","unstructured":"Kinjo AR, Nishikawa K: Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks. Biophysics 2005, 1: 67\u201374. 10.2142\/biophysics.1.67","journal-title":"Biophysics"},{"key":"2240_CR20","doi-asserted-by":"publisher","first-page":"1955","DOI":"10.1110\/ps.051479505","volume":"14","author":"D Kihara","year":"2005","unstructured":"Kihara D: On the effect of long range interactions on secondary structure formation in proteins. Protein Science 2005, 14: 1955\u20131963. 10.1110\/ps.051479505","journal-title":"Protein Science"},{"key":"2240_CR21","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1186\/1471-2105-7-401","volume":"7","author":"AR Kinjo","year":"2006","unstructured":"Kinjo AR, Nishikawa K: CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. BMC Bioinformatics 2006, 7: 401. 10.1186\/1471-2105-7-401","journal-title":"BMC Bioinformatics"},{"key":"2240_CR22","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1186\/1471-2105-7-425","volume":"7","author":"J Song","year":"2006","unstructured":"Song J, Burrage K: Predicting residue-wise contact orders in proteins by support vector regression. BMC Bioinformatics 2006, 7: 425. 10.1186\/1471-2105-7-425","journal-title":"BMC Bioinformatics"},{"key":"2240_CR23","doi-asserted-by":"publisher","first-page":"2167","DOI":"10.1093\/bioinformatics\/bti330","volume":"21","author":"AR Kinjo","year":"2005","unstructured":"Kinjo AR, Nishikawa K: Recoverable one-dimensional encoding of three-dimensional protein structures. Bioinformatics 2005, 21: 2167\u20132170. 10.1093\/bioinformatics\/bti330","journal-title":"Bioinformatics"},{"key":"2240_CR24","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1002\/prot.20300","volume":"58","author":"AR Kinjo","year":"2005","unstructured":"Kinjo AR, Horimoto K, Nishikawa K: Predicting absolute contact numbers of native protein structure from amino acid sequence. Proteins 2005, 58: 158\u2013165. 10.1002\/prot.20300","journal-title":"Proteins"},{"key":"2240_CR25","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1093\/bioinformatics\/17.2.202","volume":"17","author":"P Fariselli","year":"2001","unstructured":"Fariselli P, Casadio R: RCNPRED: prediction of the residue co-ordination numbers in proteins. Bioinformatics 2001, 17: 202\u2013204. 10.1093\/bioinformatics\/17.2.202","journal-title":"Bioinformatics"},{"key":"2240_CR26","doi-asserted-by":"publisher","first-page":"S234","DOI":"10.1093\/bioinformatics\/17.suppl_1.S234","volume":"17","author":"G Pollastri","year":"2001","unstructured":"Pollastri G, Baldi P, Fariselli P, Casadio R: Improved prediction of the number of residue contacts in proteins by recurrent neural networks. Bioinformatics 2001, 17: S234-S242.","journal-title":"Bioinformatics"},{"key":"2240_CR27","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1002\/prot.10069","volume":"47","author":"G Pollastri","year":"2002","unstructured":"Pollastri G, Baldi P, Fariselli P, Casadio R: Prediction of coordination number and relative solvent accessibility in proteins. Proteins 2002, 47: 142\u2013153. 10.1002\/prot.10069","journal-title":"Proteins"},{"key":"2240_CR28","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1002\/prot.21047","volume":"64","author":"T Ishida","year":"2006","unstructured":"Ishida T, Nakamura S, Shimizu K: Potential for assessing quality of protein structure based on contact number prediction. Proteins 2006, 64: 940\u2013947. 10.1002\/prot.21047","journal-title":"Proteins"},{"key":"2240_CR29","volume-title":"Machine Learning","author":"T Mitchell","year":"1997","unstructured":"Mitchell T: Machine Learning. McGraw Hill; 1997."},{"key":"2240_CR30","unstructured":"Calculate the Contact Order of Proteins[http:\/\/depts.washington.edu\/bakerpg\/contact_order\/]"},{"key":"2240_CR31","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1186\/1471-2105-7-301","volume":"7","author":"S Montgomerie","year":"2006","unstructured":"Montgomerie S, Sundararaj S, Gallin W, Wishart DS: Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics 2006, 7: 301. 10.1186\/1471-2105-7-301","journal-title":"BMC Bioinformatics"},{"key":"2240_CR32","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","volume":"19","author":"G Wang","year":"2003","unstructured":"Wang G, Dunbrack RL Jr: PISCES: a protein sequence culling server. Bioinformatics 2003, 19: 1589\u20131591. 10.1093\/bioinformatics\/btg224","journal-title":"Bioinformatics"},{"key":"2240_CR33","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of Molecular Biology 1990, 215: 403\u2013410.","journal-title":"Journal of Molecular Biology"},{"key":"2240_CR34","doi-asserted-by":"publisher","first-page":"3316","DOI":"10.1093\/nar\/gkg565","volume":"31","author":"L Willard","year":"2003","unstructured":"Willard L, Ranjan A, Zhang H, Monzavi H, Boyko RF, Sykes BD, Wishart DS: VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Research 2003, 31: 3316\u20133319. 10.1093\/nar\/gkg565","journal-title":"Nucleic Acids Research"},{"key":"2240_CR35","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkm800","volume":"36","author":"DS Wishart","year":"2008","unstructured":"Wishart DS, Arndt D, Berjanskii M, Guo AC, Shi Y, Shrivastava S, Zhou J, Zhu Y, Lin GH: PPT-DB: The Protein Property Prediction and Testing Database. Nucleic Acids Research 2008, 36: D222-D229. 10.1093\/nar\/gkm800","journal-title":"Nucleic Acids Research"},{"key":"2240_CR36","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1023\/B:STCO.0000035301.49549.88","volume":"14","author":"AJ Smola","year":"2003","unstructured":"Smola AJ, Sch\u00f6lkopf B: A tutorial on support vector regression. Statistics and Computing 2003, 14: 199\u2013222. 10.1023\/B:STCO.0000035301.49549.88","journal-title":"Statistics and Computing"},{"key":"2240_CR37","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/3905.001.0001","volume-title":"An Introduction to Neural Networks","author":"JA Anderson","year":"1995","unstructured":"Anderson JA: An Introduction to Neural Networks. MIT Press; 1995."},{"key":"2240_CR38","unstructured":"Protein Contact Order Prediction\/Calculation Web Sever[http:\/\/www.copredictor.ca]"},{"key":"2240_CR39","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 Research 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Research"},{"key":"2240_CR40","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 TJP, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 2004, 32: D226-D229. 10.1093\/nar\/gkh039","journal-title":"Nucleic Acids Research"},{"key":"2240_CR41","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1093\/protein\/11.9.739","volume":"11","author":"IN Shindyalov","year":"1998","unstructured":"Shindyalov IN, Bourne PE: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 1998, 11: 739\u2013747. 10.1093\/protein\/11.9.739","journal-title":"Protein Engineering"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-255.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:24:44Z","timestamp":1630466684000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-255"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,30]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2240"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-255","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,30]]},"assertion":[{"value":"20 August 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"255"}}