{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T06:27:35Z","timestamp":1774592855927,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Protein secondary structure and solvent accessibility predictions are a fundamental intermediate step towards protein structure and function prediction. We present new systems for the ab initio prediction of protein secondary structure and solvent accessibility, Porter 4.0 and PaleAle 4.0. Porter 4.0 predicts secondary structure correctly for 82.2% of residues. PaleAle 4.0\u2019s accuracy is 80.0% for prediction in two classes with a 25% accessibility threshold. We show that the increasing training set sizes that come with the continuing growth of the Protein Data Bank keep yielding prediction quality improvements and examine the impact of protein resolution on prediction performances.<\/jats:p>\n               <jats:p>Availability: Porter 4.0 and PaleAle 4.0 are freely available for academic users at http:\/\/distillf.ucd.ie\/porterpaleale\/. Up to 64 kb of input in FASTA format can be processed in a single submission, with predictions now being returned to the user within a single web page and, optionally, a single email.<\/jats:p>\n               <jats:p>Contact: \u00a0gianluca.pollastri@ucd.ie<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt344","type":"journal-article","created":{"date-parts":[[2013,6,15]],"date-time":"2013-06-15T02:25:10Z","timestamp":1371263110000},"page":"2056-2058","source":"Crossref","is-referenced-by-count":108,"title":["Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility"],"prefix":"10.1093","volume":"29","author":[{"given":"Claudio","family":"Mirabello","sequence":"first","affiliation":[{"name":"1 School of Computer Science and Informatics and 2Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland"},{"name":"1 School of Computer Science and Informatics and 2Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gianluca","family":"Pollastri","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and Informatics and 2Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland"},{"name":"1 School of Computer Science and Informatics and 2Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,6,14]]},"reference":[{"key":"2023020305301859500_btt344-B1","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":"2023020305301859500_btt344-B2","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1093\/bioinformatics\/15.11.937","article-title":"Exploiting the past and the future in protein secondary structure prediction","volume":"15","author":"Baldi","year":"1999","journal-title":"Bioinformatics"},{"key":"2023020305301859500_btt344-B3","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1002\/pro.5560050516","article-title":"Protein fold recognition using sequence-derived predictions","volume":"5","author":"Fischer","year":"1996","journal-title":"Protein Sci."},{"key":"2023020305301859500_btt344-B4","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2023020305301859500_btt344-B5","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/prot.22429","article-title":"Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information","volume":"77","author":"Mooney","year":"2009","journal-title":"Proteins"},{"key":"2023020305301859500_btt344-B6","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1093\/bioinformatics\/btt103","article-title":"PeptideLocator: prediction of bioactive peptides in protein sequences","volume":"29","author":"Mooney","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020305301859500_btt344-B7","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.jmb.2005.02.025","article-title":"Mimicking cellular sorting improves prediction of subcellular localization","volume":"348","author":"Nair","year":"2005","journal-title":"J. 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