{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T17:32:06Z","timestamp":1725471126583},"publisher-location":"Berlin, Heidelberg","reference-count":23,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642341229"},{"type":"electronic","value":"9783642341236"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-34123-6_3","type":"book-chapter","created":{"date-parts":[[2012,11,4]],"date-time":"2012-11-04T00:52:31Z","timestamp":1351990351000},"page":"26-37","source":"Crossref","is-referenced-by-count":0,"title":["A Genetic Algorithm for Scale-Based Translocon Simulation"],"prefix":"10.1007","author":[{"given":"Sami","family":"Laroum","sequence":"first","affiliation":[]},{"given":"B\u00e9atrice","family":"Duval","sequence":"additional","affiliation":[]},{"given":"Dominique","family":"Tessier","sequence":"additional","affiliation":[]},{"given":"Jin-Kao","family":"Hao","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"4","key":"3_CR1","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","volume":"340","author":"J.D. Bendtsen","year":"2004","unstructured":"Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S.: Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology\u00a0340(4), 783\u2013795 (2004)","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"3_CR2","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"H.M. Berman","year":"2000","unstructured":"Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research\u00a028(1), 235\u2013242 (2000)","journal-title":"Nucleic Acids Research"},{"issue":"20","key":"3_CR3","doi-asserted-by":"publisher","first-page":"7177","DOI":"10.1073\/pnas.0711151105","volume":"105","author":"A. Bernsel","year":"2008","unstructured":"Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G., Elofsson, A.: Prediction of membrane-protein topology from first principles. Proceedings of the National Academy of Sciences of the Unites States of America\u00a0105(20), 7177\u20137181 (2008)","journal-title":"Proceedings of the National Academy of Sciences of the Unites States of America"},{"issue":"6","key":"3_CR4","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1093\/protein\/gzi032","volume":"18","author":"J.M. Cuthbertson","year":"2005","unstructured":"Cuthbertson, J.M., Doyle, D.A., Sansom, M.S.P.: Transmembrane helix prediction: a comparative evaluation and analysis. Protein Engineering Design and Selection\u00a018(6), 295\u2013308 (2005)","journal-title":"Protein Engineering Design and Selection"},{"issue":"5881","key":"3_CR5","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1038\/299371a0","volume":"299","author":"D. Eisenberg","year":"1982","unstructured":"Eisenberg, D., Weiss, R.M., Terwilliger, T.C.: The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature\u00a0299(5881), 371\u2013374 (1982)","journal-title":"Nature"},{"key":"3_CR6","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1146\/annurev.bb.15.060186.001541","volume":"15","author":"D.M. Engelman","year":"1986","unstructured":"Engelman, D.M., Steitz, T.A., Goldman, A.: Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annual Review of Biophysics and Biophysical Chemistry\u00a015, 321\u2013353 (1986)","journal-title":"Annual Review of Biophysics and Biophysical Chemistry"},{"key":"3_CR7","unstructured":"Goldberg, D.E.: Genetic Algorithms in Search, Optimization, and Machine Learning, 1st edn. Addison-Wesley (January 1989)"},{"issue":"7024","key":"3_CR8","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/nature03216","volume":"433","author":"T. Hessa","year":"2005","unstructured":"Hessa, T., Kim, H., Bihlmaier, K., Lundin, C., Boekel, J., Andersson, H., Nilsson, I., White, S.H., von Heijne, G.: Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature\u00a0433(7024), 377\u2013381 (2005)","journal-title":"Nature"},{"issue":"7172","key":"3_CR9","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nature06387","volume":"450","author":"T. Hessa","year":"2007","unstructured":"Hessa, T., Meindl-Beinker, N.M., Bernsel, A., Kim, H., Sato, Y., Lerch-Bader, M., Nilsson, I., White, S.H., von Heijne, G.: Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450(7172), 1026\u2013U2 (2007)","journal-title":"Nature"},{"issue":"5","key":"3_CR10","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1093\/bioinformatics\/btl677","volume":"23","author":"D.T. Jones","year":"2007","unstructured":"Jones, D.T.: Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics\u00a023(5), 538\u2013544 (2007)","journal-title":"Bioinformatics"},{"issue":"10","key":"3_CR11","doi-asserted-by":"publisher","first-page":"3038","DOI":"10.1021\/bi00176a037","volume":"33","author":"D.T. Jones","year":"1994","unstructured":"Jones, D.T., Taylor, W.R., Thorton, J.M.: A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry\u00a033(10), 3038\u20133049 (1994)","journal-title":"Biochemistry"},{"issue":"12","key":"3_CR12","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1093\/bioinformatics\/15.12.1066","volume":"15","author":"V.L. Junker","year":"1999","unstructured":"Junker, V.L., Apweiler, R., Bairoch, A.: Representation of functional information in the SWISS-PROT data bank. Bioinformatics\u00a015(12), 1066\u20131067 (1999)","journal-title":"Bioinformatics"},{"key":"3_CR13","doi-asserted-by":"crossref","unstructured":"Kall, L.: Prediction of transmembrane topology and signal peptide given a protein\u2019s amino acid sequence. Method. In: Molecular Biology, vol.\u00a0673, pp. 53\u201362 (2010)","DOI":"10.1007\/978-1-60761-842-3_4"},{"issue":"5","key":"3_CR14","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","volume":"338","author":"L. Kall","year":"2004","unstructured":"Kall, L., Krogh, A., Sonnhammer, E.L.L.: A combined transmembrane topology and signal peptide prediction method. Journal of Molecular Biology\u00a0338(5), 1027\u20131036 (2004)","journal-title":"Journal of Molecular Biology"},{"issue":"3","key":"3_CR15","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A. Krogh","year":"2001","unstructured":"Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L.L.: Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. Journal of Molecular Biology\u00a0305(3), 567\u2013580 (2001)","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"3_CR16","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0022-2836(82)90515-0","volume":"157","author":"J. Kyte","year":"1982","unstructured":"Kyte, J., Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology\u00a0157(1), 105\u2013132 (1982)","journal-title":"Journal of Molecular Biology"},{"key":"3_CR17","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/978-3-642-20389-3_11","volume-title":"EvoBio 2011","author":"S. Laroum","year":"2011","unstructured":"Laroum, S., Duval, B., Tessier, D., Hao, J.-K.: Multi-Neighborhood Search for Discrimination of Signal Peptides and Transmembrane Segments. In: Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds.) EvoBIO 2011. LNCS, vol.\u00a06623, pp. 111\u2013122. Springer, Heidelberg (2011)"},{"issue":"5","key":"3_CR18","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/protein\/12.5.381","volume":"12","author":"C. Pasquier","year":"1999","unstructured":"Pasquier, C., Promponas, V.J., Palaios, G.A., Hamodrakas, J.S., Hamodrakas, S.J.: A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Engineering\u00a012(5), 381\u2013385 (1999)","journal-title":"Protein Engineering"},{"key":"3_CR19","doi-asserted-by":"crossref","unstructured":"Reynolds, S.M., Kaell, L., Riffle, M.E., Bilmes, J.A., Noble, W.S.: Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. Plos Computational Biology 4(11) (2008)","DOI":"10.1371\/journal.pcbi.1000213"},{"issue":"8","key":"3_CR20","doi-asserted-by":"publisher","first-page":"1704","DOI":"10.1002\/pro.5560050824","volume":"5","author":"B. Rost","year":"1996","unstructured":"Rost, B., Fariselli, P., Casadio, R.: Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science\u00a05(8), 1704\u20131718 (1996)","journal-title":"Protein Science"},{"issue":"9","key":"3_CR21","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1093\/bioinformatics\/17.9.849","volume":"17","author":"G.E. Tusnady","year":"2001","unstructured":"Tusnady, G.E., Simon, I.: The HMMTOP transmembrane topology prediction server. Bioinformatics\u00a017(9), 849\u2013850 (2001)","journal-title":"Bioinformatics"},{"issue":"24","key":"3_CR22","doi-asserted-by":"publisher","first-page":"2928","DOI":"10.1093\/bioinformatics\/btn550","volume":"24","author":"H. Viklund","year":"2008","unstructured":"Viklund, H., Bernsel, A., Skwark, M., Elofsson, A.: SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics\u00a024(24), 2928\u20132929 (2008)","journal-title":"Bioinformatics"},{"key":"3_CR23","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1146\/annurev.biophys.37.032807.125904","volume":"37","author":"S.H. White","year":"2008","unstructured":"White, S.H., von Heijne, G.: How translocons select transmembrane helices. Annual Review of Biophysics\u00a037, 23\u201342 (2008)","journal-title":"Annual Review of Biophysics"}],"container-title":["Lecture Notes in Computer Science","Pattern Recognition in Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-34123-6_3.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T12:45:38Z","timestamp":1620132338000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-34123-6_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642341229","9783642341236"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-34123-6_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}