{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:21:41Z","timestamp":1761862901702},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Transmembrane \u03b2-barrels (TMBBs) belong to a special structural class of proteins predominately found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. TMBBs are surface-exposed proteins that perform a variety of functions ranging from nutrient acquisition to osmotic regulation. These properties suggest that TMBBs have great potential for use in vaccine or drug therapy development. However, membrane proteins, such as TMBBs, are notoriously difficult to identify and characterize using traditional experimental approaches and current prediction methods are still unreliable.<\/jats:p>\n               <jats:p>Results: A prediction method based on the physicochemical properties of experimentally characterized TMBB structures was developed to predict TMBB-encoding genes from genomic databases. The Freeman\u2013Wimley prediction algorithm developed in this study has an accuracy of 99% and MCC of 0.748 when using the most efficient prediction criteria, which is better than any previously published algorithm.<\/jats:p>\n               <jats:p>Availability: The MS Windows-compatible application is available for download at http:\/\/www.tulane.edu\/\u223cbiochem\/WW\/apps.html<\/jats:p>\n               <jats:p>Contact: \u00a0wwimley@tulane.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq308","type":"journal-article","created":{"date-parts":[[2010,6,11]],"date-time":"2010-06-11T00:51:37Z","timestamp":1276217497000},"page":"1965-1974","source":"Crossref","is-referenced-by-count":47,"title":["A highly accurate statistical approach for the prediction of transmembrane \u03b2-barrels"],"prefix":"10.1093","volume":"26","author":[{"suffix":"Jr.","given":"Thomas C.","family":"Freeman","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Tulane University Health Sciences Center, New Orleans, LA 70112, USA"}]},{"given":"William C.","family":"Wimley","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Tulane University Health Sciences Center, New Orleans, LA 70112, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,10]]},"reference":[{"key":"2023012508025251000_B1","doi-asserted-by":"crossref","first-page":"52816","DOI":"10.1074\/jbc.C400445200","article-title":"Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end","volume":"279","author":"Akama","year":"2004","journal-title":"J. Biol. Chem."},{"key":"2023012508025251000_B2","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/S0065-3233(08)60413-1","article-title":"Experimental and theoretical aspects of protein folding","volume":"29","author":"Anfinsen","year":"1975","journal-title":"Adv. Protein Chem."},{"key":"2023012508025251000_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":"2023012508025251000_B4","doi-asserted-by":"crossref","first-page":"W394","DOI":"10.1093\/nar\/gkh351","article-title":"BOMP: a program to predict integral \u03b2-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria","volume":"32","author":"Berven","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012508025251000_B5","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/nsb914","article-title":"Substrate-induced transmembrane signaling in the cobalamin transporter BtuB","volume":"10","author":"Chimento","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"2023012508025251000_B6","doi-asserted-by":"crossref","first-page":"2358","DOI":"10.1073\/pnas.051629298","article-title":"Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles","volume":"98","author":"Fernandez","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA."},{"key":"2023012508025251000_B7","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1002\/prot.20929","article-title":"Discrimination of outer membrane proteins using machine learning algorithms","volume":"63","author":"Gromiha","year":"2006","journal-title":"Proteins"},{"key":"2023012508025251000_B8","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.compbiolchem.2008.03.010","article-title":"A method for discovering transmembrane \u03b2-barrel proteins in Gram-negative bacterial proteomes","volume":"32","author":"Hu","year":"2008","journal-title":"Comput. Biol. Chem."},{"key":"2023012508025251000_B9","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1006\/jmbi.2001.5008","article-title":"Energetics, stability, and prediction of transmembrane helices","volume":"312","author":"Jayasinghe","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012508025251000_B10","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/35016007","article-title":"Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export","volume":"405","author":"Koronakis","year":"2000","journal-title":"Nature"},{"key":"2023012508025251000_B11","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/S1476-9271(02)00085-3","article-title":"Identification of \u03b2-barrel membrane proteins based on amino acid composition properties and predicted secondary structure","volume":"27","author":"Liu","year":"2003","journal-title":"Comput. Biol. Chem."},{"key":"2023012508025251000_B12","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochim. Biophys. Acta"},{"key":"2023012508025251000_B13","doi-asserted-by":"crossref","first-page":"2297","DOI":"10.1038\/sj.emboj.7601132","article-title":"Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter","volume":"25","author":"Meng","year":"2006","journal-title":"EMBO J."},{"key":"2023012508025251000_B14","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/nsmb827","article-title":"Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation","volume":"11","author":"Mowat","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012508025251000_B15","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"Murzin","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2023012508025251000_B16","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1038\/sj.emboj.7600148","article-title":"Structure of the translocator domain of a bacterial autotransporter","volume":"23","author":"Oomen","year":"2004","journal-title":"EMBO J."},{"key":"2023012508025251000_B17","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.compbiolchem.2008.03.002","article-title":"TMBETADISC-RBF: discrimination of \u03b2-barrel membrane proteins using RBF networks and PSSM profiles","volume":"32","author":"Ou","year":"2008","journal-title":"Comput. Biol. Chem."},{"key":"2023012508025251000_B18","doi-asserted-by":"crossref","first-page":"11238","DOI":"10.1021\/bi001139p","article-title":"Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action","volume":"39","author":"Parsiegla","year":"2000","journal-title":"Biochemistry"},{"key":"2023012508025251000_B19","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1038\/2983","article-title":"Structure of the outer membrane protein A transmembrane domain","volume":"5","author":"Pautsch","year":"1998","journal-title":"Nat. Struct. Biol."},{"key":"2023012508025251000_B20","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1016\/j.cell.2008.03.033","article-title":"Fiber formation across the bacterial outer membrane by the chaperone\/usher pathway","volume":"133","author":"Remaut","year":"2008","journal-title":"Cell"},{"key":"2023012508025251000_B21","doi-asserted-by":"crossref","first-page":"D164","DOI":"10.1093\/nar\/gki027","article-title":"PSORTdb: a protein subcellular localization database for bacteria","volume":"33","author":"Rey","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012508025251000_B22","doi-asserted-by":"crossref","first-page":"7071","DOI":"10.1073\/pnas.0509392103","article-title":"Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa","volume":"103","author":"Rutten","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA."},{"key":"2023012508025251000_B23","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1006\/jmbi.2001.4583","article-title":"The X-ray crystal structure of the Trichoderma reesei family 12 endoglucanase 3, Cel12A, at 1.9 A resolution","volume":"308","author":"Sandgren","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012508025251000_B24","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/S0959-440X(00)00120-2","article-title":"\u03b2-Barrel membrane proteins","volume":"10","author":"Schulz","year":"2000","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012508025251000_B25","doi-asserted-by":"crossref","first-page":"2624","DOI":"10.1002\/pro.256","article-title":"MPEx: a tool for exploring membrane proteins","volume":"18","author":"Snider","year":"2009","journal-title":"Protein Sci."},{"key":"2023012508025251000_B26","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1126\/science.274.5294.1859","article-title":"Structure of staphylococcal \u03b1-hemolysin, a heptameric transmembrane pore","volume":"274","author":"Song","year":"1996","journal-title":"Science"},{"key":"2023012508025251000_B27","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1093\/emboj\/20.18.5033","article-title":"Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site","volume":"20","author":"Vandeputte-Rutten","year":"2001","journal-title":"EMBO J."},{"key":"2023012508025251000_B28","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1016\/S0969-2126(00)80063-5","article-title":"The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence","volume":"7","author":"Vogt","year":"1999","journal-title":"Structure"},{"key":"2023012508025251000_B29","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1002\/pro.5560030312","article-title":"Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase","volume":"3","author":"Wakarchuk","year":"1994","journal-title":"Protein Sci."},{"key":"2023012508025251000_B30","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1006\/jmbi.1997.1224","article-title":"Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin","volume":"272","author":"Wang","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023012508025251000_B31","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/S0304-4157(98)00021-5","article-title":"Hydrophobic interactions of peptides with membrane interfaces","volume":"1376","author":"White","year":"1998","journal-title":"Biochim. Biophys. Acta"},{"key":"2023012508025251000_B32","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1110\/ps.29402","article-title":"Toward genomic identification of \u03b2-barrel membrane proteins: composition and architecture of known structures","volume":"11","author":"Wimley","year":"2002","journal-title":"Protein Sci."},{"key":"2023012508025251000_B33","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/S0959-440X(03)00099-X","article-title":"The versatile \u03b2-barrel membrane protein","volume":"13","author":"Wimley","year":"2003","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012508025251000_B34","doi-asserted-by":"crossref","first-page":"3187","DOI":"10.1038\/sj.emboj.7600330","article-title":"Crystal structure of the bacterial nucleoside transporter Tsx","volume":"23","author":"Ye","year":"2004","journal-title":"EMBO J."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/16\/1965\/48855135\/bioinformatics_26_16_1965.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/16\/1965\/48855135\/bioinformatics_26_16_1965.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:03:53Z","timestamp":1674633833000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/16\/1965\/215152"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,10]]},"references-count":34,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2010,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq308","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,8,15]]},"published":{"date-parts":[[2010,6,10]]}}}