{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T03:46:03Z","timestamp":1793418363091,"version":"4.5.0"},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,2,19]],"date-time":"2005-02-19T00:00:00Z","timestamp":1108771200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,2,19]],"date-time":"2005-02-19T00:00:00Z","timestamp":1108771200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Detection of DNA-binding sites in proteins is of enormous interest for technologies targeting gene regulation and manipulation. We have previously shown that a residue and its sequence neighbor information can be used to predict DNA-binding candidates in a protein sequence. This sequence-based prediction method is applicable even if no sequence homology with a previously known DNA-binding protein is observed. Here we implement a neural network based algorithm to utilize evolutionary information of amino acid sequences in terms of their position specific scoring matrices (PSSMs) for a better prediction of DNA-binding sites.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>An average of sensitivity and specificity using PSSMs is up to 8.7% better than the prediction with sequence information only. Much smaller data sets could be used to generate PSSM with minimal loss of prediction accuracy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>One problem in using PSSM-derived prediction is obtaining lengthy and time-consuming alignments against large sequence databases. In order to speed up the process of generating PSSMs, we tried to use different reference data sets (sequence space) against which a target protein is scanned for PSI-BLAST iterations. We find that a very small set of proteins can actually be used as such a reference data without losing much of the prediction value. This makes the process of generating PSSMs very rapid and even amenable to be used at a genome level. A web server has been developed to provide these predictions of DNA-binding sites for any new protein from its amino acid sequence.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>\n                      Online predictions based on this method are available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.netasa.org\/dbs-pssm\/\">http:\/\/www.netasa.org\/dbs-pssm\/<\/jats:ext-link>\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2105-6-33","type":"journal-article","created":{"date-parts":[[2005,2,19]],"date-time":"2005-02-19T02:25:37Z","timestamp":1108779937000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":234,"title":["PSSM-based prediction of DNA binding sites in proteins"],"prefix":"10.1186","volume":"6","author":[{"given":"Shandar","family":"Ahmad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akinori","family":"Sarai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2005,2,19]]},"reference":[{"key":"358_CR1","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1093\/nar\/26.10.2306","volume":"26","author":"MY Gutfreund","year":"1998","unstructured":"Gutfreund MY, Margalit H: Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. 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