{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:15:11Z","timestamp":1760955311557},"reference-count":31,"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>With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in <jats:italic>Escherichia coli<\/jats:italic> and <jats:italic>Saccharomyces cerevisiae<\/jats:italic> respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-409","type":"journal-article","created":{"date-parts":[[2011,10,25]],"date-time":"2011-10-25T06:27:37Z","timestamp":1319524057000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation"],"prefix":"10.1186","volume":"12","author":[{"given":"Xianwen","family":"Ren","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong-Cui","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiang-Sun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nai-Yang","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,10,24]]},"reference":[{"issue":"6230","key":"4877_CR1","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/340245a0","volume":"340","author":"S Fields","year":"1989","unstructured":"Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 1989, 340(6230):245\u2013246. 10.1038\/340245a0","journal-title":"Nature"},{"issue":"6","key":"4877_CR2","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1039\/b212800b","volume":"128","author":"JR Engen","year":"2003","unstructured":"Engen JR: Analysis of protein complexes with hydrogen exchange and mass spectrometry. Analyst 2003, 128(6):623\u2013628. 10.1039\/b212800b","journal-title":"Analyst"},{"issue":"6868","key":"4877_CR3","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat C-M, et al.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415(6868):141\u2013147. 10.1038\/415141a","journal-title":"Nature"},{"issue":"1","key":"4877_CR4","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/S0959-440X(98)80019-5","volume":"8","author":"JH Lakey","year":"1998","unstructured":"Lakey JH, Raggett EM: Measuring protein-protein interactions. Current Opinion in Structural Biology 1998, 8(1):119\u2013123. 10.1016\/S0959-440X(98)80019-5","journal-title":"Current Opinion in Structural Biology"},{"issue":"5537","key":"4877_CR5","doi-asserted-by":"publisher","first-page":"2101","DOI":"10.1126\/science.1062191","volume":"293","author":"H Zhu","year":"2001","unstructured":"Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, et al.: Global Analysis of Protein Activities Using Proteome Chips. Science 2001, 293(5537):2101\u20132105. 10.1126\/science.1062191","journal-title":"Science"},{"issue":"7025","key":"4877_CR6","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1038\/nature03239","volume":"433","author":"G Butland","year":"2005","unstructured":"Butland G, Peregr\u00c3n-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, et al.: Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005, 433(7025):531\u2013537. 10.1038\/nature03239","journal-title":"Nature"},{"issue":"6817","key":"4877_CR7","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/35051615","volume":"409","author":"JC Rain","year":"2001","unstructured":"Rain JC, Selig L, Reuse HD, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, et al.: The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409(6817):211\u2013215. 10.1038\/35051615","journal-title":"Nature"},{"issue":"6770","key":"4877_CR8","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623\u2013627. 10.1038\/35001009","journal-title":"Nature"},{"issue":"8","key":"4877_CR9","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","volume":"98","author":"T Ito","year":"2001","unstructured":"Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(8):4569\u20134574. 10.1073\/pnas.061034498","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"5657","key":"4877_CR10","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1126\/science.1091403","volume":"303","author":"S Li","year":"2004","unstructured":"Li S: A Map of the Interactome Network of the Metazoan C. elegans. Science 2004, 303(5657):540\u2013543. 10.1126\/science.1091403","journal-title":"Science"},{"issue":"5651","key":"4877_CR11","doi-asserted-by":"publisher","first-page":"1727","DOI":"10.1126\/science.1090289","volume":"302","author":"L Giot","year":"2003","unstructured":"Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, et al.: A Protein Interaction Map of Drosophila melanogaster. Science 2003, 302(5651):1727\u20131736. 10.1126\/science.1090289","journal-title":"Science"},{"issue":"6","key":"4877_CR12","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","volume":"122","author":"U Stelzl","year":"2005","unstructured":"Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al.: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957\u2013968. 10.1016\/j.cell.2005.08.029","journal-title":"Cell"},{"issue":"7062","key":"4877_CR13","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1038\/nature04209","volume":"437","author":"JF Rual","year":"2005","unstructured":"Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, et al.: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437(7062):1173\u20131178. 10.1038\/nature04209","journal-title":"Nature"},{"issue":"6887","key":"4877_CR14","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C von Mering","year":"2002","unstructured":"von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399\u2013403.","journal-title":"Nature"},{"issue":"11","key":"4877_CR15","doi-asserted-by":"publisher","first-page":"4337","DOI":"10.1073\/pnas.0607879104","volume":"104","author":"J Shen","year":"2007","unstructured":"Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H: Predicting protein-protein interactions based only on sequences information. Proceedings of the National Academy of Sciences 2007, 104(11):4337\u20134341. 10.1073\/pnas.0607879104","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"suppl1","key":"4877_CR16","doi-asserted-by":"publisher","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","volume":"21","author":"A Ben-Hur","year":"2005","unstructured":"Ben-Hur A: Kernel methods for predicting protein-protein interactions. Bioinformatics 2005, 21(suppl1):i38-i46.","journal-title":"Bioinformatics"},{"issue":"15","key":"4877_CR17","doi-asserted-by":"publisher","first-page":"1875","DOI":"10.1093\/bioinformatics\/btg352","volume":"19","author":"SM Gomez","year":"2003","unstructured":"Gomez SM, Noble WS, Rzhetsky A: Learning to predict protein-protein interactions from protein sequences. Bioinformatics 2003, 19(15):1875\u20131881. 10.1093\/bioinformatics\/btg352","journal-title":"Bioinformatics"},{"issue":"5","key":"4877_CR18","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1093\/bioinformatics\/17.5.455","volume":"17","author":"JR Bock","year":"2001","unstructured":"Bock JR, Gough DA: Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17(5):455\u2013460. 10.1093\/bioinformatics\/17.5.455","journal-title":"Bioinformatics"},{"issue":"5","key":"4877_CR19","doi-asserted-by":"publisher","first-page":"R87","DOI":"10.1186\/gb-2008-9-5-r87","volume":"9","author":"H Najafabadi","year":"2008","unstructured":"Najafabadi H, Salavati R: Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biology 2008, 9(5):R87. 10.1186\/gb-2008-9-5-r87","journal-title":"Genome Biology"},{"key":"4877_CR20","first-page":"564","volume-title":"Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing","author":"C Leslie","year":"2002","unstructured":"Leslie C, Eskin E, Noble WS: The spectrum kernel: a string kernel for SVM protein classification. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing 2002, 564\u2013575."},{"key":"4877_CR21","first-page":"282","volume":"25","author":"L Luo","year":"2009","unstructured":"Luo L, Zhang Sw, Chen W, Pan Q: Predicting protein-protein interaction based on the sequence-segmented amino acid composition. ACTA BIOPHYSICA SINICA 2009, 25: 282\u2013286.","journal-title":"ACTA BIOPHYSICA SINICA"},{"key":"4877_CR22","volume-title":"Lehninger Principles of Biochemistry","author":"D Nelson","year":"2004","unstructured":"Nelson D, Cox M: Lehninger Principles of Biochemistry. In Fourth edition. Edited by: W. H. Freeman. 2004.","edition":"Fourth"},{"issue":"2","key":"4877_CR23","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai Z: Network biology: understanding the cell's functional organization. Nature Reviews Genetics 2004, 5(2):101\u2013113. 10.1038\/nrg1272","journal-title":"Nature Reviews Genetics"},{"issue":"2","key":"4877_CR24","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1093\/bioinformatics\/bth483","volume":"21","author":"S Martin","year":"2005","unstructured":"Martin S, Roe D, Faulon JL: Predicting protein-protein interactions using signature products. Bioinformatics 2005, 21(2):218\u2013226. 10.1093\/bioinformatics\/bth483","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"4877_CR25","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-7-S1-S2","volume":"7","author":"A Ben-Hur","year":"2006","unstructured":"Ben-Hur A, Noble WS: Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 2006, 7(Suppl 1):S2. 10.1186\/1471-2105-7-S1-S2","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"4877_CR26","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1186\/1471-2105-9-192","volume":"9","author":"M Jiang","year":"2008","unstructured":"Jiang M, Anderson J, Gillespie J, Mayne M: uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics 2008, 9(1):192\u2013192. 10.1186\/1471-2105-9-192","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"4877_CR27","doi-asserted-by":"publisher","first-page":"3025","DOI":"10.1093\/nar\/gkn159","volume":"36","author":"Y Guo","year":"2008","unstructured":"Guo Y, Yu L, Wen Z, Li M: Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Research 2008, 36(9):3025\u20133030. 10.1093\/nar\/gkn159","journal-title":"Nucleic Acids Research"},{"key":"4877_CR28","first-page":"144","volume-title":"5th Annual ACM Workshop on COLT","author":"BE Boser","year":"1992","unstructured":"Boser BE, Guyon IM, Vapnik VN: A Training Algorithm for Optimal Margin Classifiers. 5th Annual ACM Workshop on COLT 1992, 144\u2013152."},{"issue":"20","key":"4877_CR29","doi-asserted-by":"publisher","first-page":"2610","DOI":"10.1093\/bioinformatics\/btq483","volume":"26","author":"J Yu","year":"2010","unstructured":"Yu J, Guo M, Needham CJ, Huang Y, Cai L, Westhead DR: Simple sequence-based kernels do not predict protein-protein interactions. Bioinformatics 2010, 26(20):2610\u20132614. 10.1093\/bioinformatics\/btq483","journal-title":"Bioinformatics"},{"key":"4877_CR30","first-page":"gkn892","volume-title":"Nucl Acids Res","author":"TSK Prasad","year":"2008","unstructured":"Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al.: Human Protein Reference Database--2009 update. Nucl Acids Res 2008, gkn892."},{"issue":"3","key":"4877_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/1961189.1961199","volume":"2","author":"CC Chang","year":"2011","unstructured":"Chang CC, Lin CJ: LIBSVM: A library for support vector machines. ACM Trans Intell Syst Technol 2011, 2(3):1\u201327.","journal-title":"ACM Trans Intell Syst Technol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-409.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T17:31:55Z","timestamp":1630517515000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-409"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,24]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4877"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-409","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,24]]},"assertion":[{"value":"29 July 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 October 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 October 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"409"}}