{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T20:37:08Z","timestamp":1720125428943},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural\/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of \u03b1-helical repeat proteins with more than 120 residues and resolution &amp;lt;2.0 \u00c5. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported.<\/jats:p>\n               <jats:p>Availability: The TESE server is available for non-commercial use at URL: http:\/\/protein.bio.unipd.it\/tese\/.<\/jats:p>\n               <jats:p>Contact: \u00a0silvio.tosatto@unipd.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn488","type":"journal-article","created":{"date-parts":[[2008,9,17]],"date-time":"2008-09-17T03:08:35Z","timestamp":1221620915000},"page":"2632-2633","source":"Crossref","is-referenced-by-count":9,"title":["TESE: generating specific protein structure test set ensembles"],"prefix":"10.1093","volume":"24","author":[{"given":"Francesco","family":"Sirocco","sequence":"first","affiliation":[{"name":"Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvio C. E.","family":"Tosatto","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,9,16]]},"reference":[{"issue":"Database issue","key":"2023020212224572700_B1","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"SCOP database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020212224572700_B2","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"2023020212224572700_B3","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1002\/pro.5560030317","article-title":"Enlarged representative set of protein structures","volume":"3","author":"Hobohm","year":"1994","journal-title":"Protein Sci."},{"key":"2023020212224572700_B4","first-page":"525","article-title":"The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value","volume":"12","author":"Hooft","year":"1996"},{"key":"2023020212224572700_B5","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s10822-008-9196-5","article-title":"Recommendations for evaluation of computational methods","volume":"22","author":"Jain","year":"2008","journal-title":"J. Comput. Aided Mol. Des."},{"key":"2023020212224572700_B6","doi-asserted-by":"crossref","first-page":"3789","DOI":"10.1093\/nar\/gkg620","article-title":"UniqueProt: creating representative protein sequence sets","volume":"31","author":"Mika","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023020212224572700_B7","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1093\/nar\/gkg022","article-title":"PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003","volume":"31","author":"Noguchi","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023020212224572700_B8","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/nar\/gkg062","article-title":"The CATH database: an extended protein family resource for structural and functional genomics","volume":"31","author":"Pearl","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023020212224572700_B9","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1471-2105-8-155","article-title":"TAP score: torsion angle propensity normalization applied to local protein structure evaluation","volume":"8","author":"Tosatto","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020212224572700_B10","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","article-title":"PISCES: a protein sequence culling server","volume":"19","author":"Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020212224572700_B11","doi-asserted-by":"crossref","first-page":"W94","DOI":"10.1093\/nar\/gki402","article-title":"PISCES: recent improvements to a PDB sequence culling server","volume":"33","author":"Wang","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2632\/49055290\/bioinformatics_24_22_2632.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2632\/49055290\/bioinformatics_24_22_2632.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T14:46:17Z","timestamp":1675349177000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/22\/2632\/184960"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,9,16]]},"references-count":11,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2008,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn488","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,11,15]]},"published":{"date-parts":[[2008,9,16]]}}}