{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T05:40:35Z","timestamp":1792820435923,"version":"4.5.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Protein insolubility is a major obstacle for many experimental studies. A sequence-based prediction method able to accurately predict the propensity of a protein to be soluble on overexpression could be used, for instance, to prioritize targets in large-scale proteomics projects and to identify mutations likely to increase the solubility of insoluble proteins.<\/jats:p>\n                  <jats:p>Results: Here, we first curate a large, non-redundant and balanced training set of more than 17 000 proteins. Next, we extract and study 23 groups of features computed directly or predicted (e.g. secondary structure) from the primary sequence. The data and the features are used to train a two-stage support vector machine (SVM) architecture. The resulting predictor, SOLpro, is compared directly with existing methods and shows significant improvement according to standard evaluation metrics, with an overall accuracy of over 74% estimated using multiple runs of 10-fold cross-validation.<\/jats:p>\n                  <jats:p>Availability: SOLpro is integrated in the SCRATCH suite of predictors and is available for download as a standalone application and as a web server at: http:\/\/scratch.proteomics.ics.uci.edu.<\/jats:p>\n                  <jats:p>Contact: \u00a0pfbaldi@ics.uci.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp386","type":"journal-article","created":{"date-parts":[[2009,6,23]],"date-time":"2009-06-23T21:31:43Z","timestamp":1245792703000},"page":"2200-2207","source":"Crossref","is-referenced-by-count":646,"title":["SOLpro: accurate sequence-based prediction of protein solubility"],"prefix":"10.1093","volume":"25","author":[{"given":"Christophe N.","family":"Magnan","sequence":"first","affiliation":[{"name":"Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arlo","family":"Randall","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Baldi","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,6,23]]},"reference":[{"key":"2023013112104261100_B1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/1475-2875-5-52","article-title":"Prediction of solubility on recombinant expression of Plasmodium falciparum erythrocyte membrane protein 1 domains in Escherichia coli","volume":"5","author":"Ahuja","year":"2006","journal-title":"Malaria J."},{"key":"2023013112104261100_B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013112104261100_B3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023013112104261100_B4","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1093\/nar\/29.13.2884","article-title":"SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics","volume":"29","author":"Bertone","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023013112104261100_B5","author":"Chang","year":"2001","journal-title":"LIBSVM: a library for support vector machines"},{"key":"2023013112104261100_B6","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1093\/bioinformatics\/bth300","article-title":"TargetDB: a target registration database for structural genomics projects","volume":"20","author":"Chen","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112104261100_B7","doi-asserted-by":"crossref","first-page":"W72","DOI":"10.1093\/nar\/gki396","article-title":"SCRATCH: a protein structure and structural feature prediction server","volume":"33","author":"Cheng","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013112104261100_B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10618-005-0023-5","article-title":"DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks","volume":"13","author":"Cheng","year":"2006","journal-title":"Data Min. Knowl. Disc."},{"key":"2023013112104261100_B9","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/82823","article-title":"Structural proteomics of an archaeon","volume":"7","author":"Christendat","year":"2000","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023013112104261100_B10","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/S0958-1669(98)80109-2","article-title":"Refolding of recombinant proteins","volume":"9","author":"Clark","year":"1998","journal-title":"Cur. Opin. Biol."},{"key":"2023013112104261100_B11","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1002\/(SICI)1097-0290(19991120)65:4<382::AID-BIT2>3.0.CO;2-I","article-title":"New fusion protein systems designed to give soluble expression in Escherichia coli","volume":"65","author":"Davis","year":"1999","journal-title":"Biotechnol. Bioeng."},{"key":"2023013112104261100_B12","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1162\/089976698300017197","article-title":"Approximate statistical tests for comparing supervised classification learning algorithms","volume":"10","author":"Dietterich","year":"1998","journal-title":"Neural Comput."},{"key":"2023013112104261100_B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/3-540-45014-9_1","article-title":"Ensemble methods in machine learning","volume":"1857","author":"Dietterich","year":"2000","journal-title":"Lect. Notes Comput. Sci."},{"key":"2023013112104261100_B14","first-page":"1889","article-title":"Working set selection using second order information for training support vector machines","volume":"6","author":"Fan","year":"2005","journal-title":"J. Mach. Learn. Res."},{"key":"2023013112104261100_B15","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.jmb.2003.11.053","article-title":"Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis","volume":"336","author":"Goh","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023013112104261100_B16","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1110\/ps.041009005","article-title":"Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli","volume":"14","author":"Idicula-Thomas","year":"2005","journal-title":"Protein Sci."},{"key":"2023013112104261100_B17","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1093\/bioinformatics\/bti810","article-title":"A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli","volume":"22","author":"Idicula-Thomas","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112104261100_B18","first-page":"1895","article-title":"Thermostability and aliphatic index of globular proteins","volume":"88","author":"Ikai","year":"1980","journal-title":"J. Biochem."},{"key":"2023013112104261100_B19","doi-asserted-by":"crossref","first-page":"1495","DOI":"10.1093\/protein\/7.12.1495","article-title":"A single amino acid substitution can restore the solubility of aggregated colicin A mutants in Escherichia coli","volume":"7","author":"Izard","year":"1994","journal-title":"Protein Eng."},{"key":"2023013112104261100_B20","first-page":"1137","article-title":"A study of cross-validation and bootstrap for accuracy estimation and model selection","volume-title":"Proceedings of the International Joint Conference on Artificial Intelligence 1995","author":"Kohavi","year":"1995"},{"key":"2023013112104261100_B21","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/S0004-3702(97)00043-X","article-title":"Wrappers for feature subset selection","volume":"97","author":"Kohavi","year":"1997","journal-title":"Artif. Intell."},{"key":"2023013112104261100_B22","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1471-2164-6-49","article-title":"How to find soluble proteins: a comprehensive analysis of alpha\/beta hydrolases for recombinant expression in E. coli","volume":"6","author":"Koschorreck","year":"2005","journal-title":"BMC Genomics"},{"key":"2023013112104261100_B23","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023013112104261100_B24","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","article-title":"A simple method for displaying the hydropathic character of a protein","volume":"157","author":"Kyte","year":"1982","journal-title":"J. Mol. Biol."},{"key":"2023013112104261100_B25","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/17.3.282","article-title":"Clustering of highly homologous sequences to reduce the size of large protein databases","volume":"17","author":"Li","year":"2001","journal-title":"Bioinformatics"},{"key":"2023013112104261100_B26","doi-asserted-by":"crossref","first-page":"2102","DOI":"10.1101\/gr.2520504","article-title":"High-throughput expression of C. elegans proteins","volume":"14","author":"Luan","year":"2004","journal-title":"Gen. Res."},{"key":"2023013112104261100_B27","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1128\/mr.60.3.512-538.1996","article-title":"Strategies for achieving high-level expression of genes in Escherichia coli","volume":"60","author":"Makrides","year":"1996","journal-title":"Microbiol. Rev."},{"key":"2023013112104261100_B28","doi-asserted-by":"crossref","first-page":"4352","DOI":"10.1046\/j.1432-1327.2001.02357.x","article-title":"Improving solubility of catalytic domain of human beta-1,4-galactosyltransferase 1 through rationally designed amino acid replacements","volume":"268","author":"Malissard","year":"2001","journal-title":"Eur. J. Biochem."},{"key":"2023013112104261100_B29","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1111\/j.1432-1033.1995.tb20531.x","article-title":"Hydrophobicity engineering to increase solubility and stability of a recombinant protein from respiratory syncytial virus","volume":"230","author":"Murby","year":"1995","journal-title":"Eur. J. Biochem."},{"key":"2023013112104261100_B30","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignments","volume":"12","author":"Rost","year":"1999","journal-title":"Protein Eng."},{"key":"2023013112104261100_B31","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1002\/cbic.200300830","article-title":"French swimwear for membrane proteins","volume":"5","author":"Sanders","year":"2004","journal-title":"ChemBioChem"},{"key":"2023013112104261100_B32","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1263\/jbb.99.303","article-title":"Solubilization and refolding of bacterial inclusion body proteins","volume":"99","author":"Singh","year":"2005","journal-title":"J. Biosci. Bioeng."},{"key":"2023013112104261100_B33","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.1093\/bioinformatics\/btl623","article-title":"Protein solubility: sequence based prediction and experimental verification","volume":"23","author":"Smialowski","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112104261100_B34","doi-asserted-by":"crossref","first-page":"D193","DOI":"10.1093\/nar\/gkl929","article-title":"The universal protein resource","volume":"35","author":"The UniProt Consortium","year":"2007","journal-title":"Nucleic Acid Res."},{"key":"2023013112104261100_B35","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1023\/B:JSFG.0000029017.46332.e3","article-title":"Refolding strategies from inclusion bodies in a structural genomics project","volume":"5","author":"Tr\u00e9saugues","year":"2004","journal-title":"J. Struct. Funct. Genomics"},{"key":"2023013112104261100_B36","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1475-2859-4-11","article-title":"Sequence determinants of protein aggregation: tools to increase protein solubility","volume":"4","author":"Ventura","year":"2005","journal-title":"Microb. Cell Fact."},{"key":"2023013112104261100_B37","first-page":"443","article-title":"Predicting the solubility of recombinant proteins in Escherichia coli","volume":"9","author":"Wilkinson","year":"1991","journal-title":"Biotechnology"},{"key":"2023013112104261100_B38","volume-title":"Data Mining: Practical Machine Learning Tools and Techniques","author":"Witten","year":"2005","edition":"2"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/17\/2200\/48993830\/bioinformatics_25_17_2200.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/17\/2200\/48993830\/bioinformatics_25_17_2200.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T16:32:44Z","timestamp":1675182764000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/17\/2200\/211163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,23]]},"references-count":38,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2009,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp386","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,9,1]]},"published":{"date-parts":[[2009,6,23]]}}}