{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T13:37:43Z","timestamp":1778074663939,"version":"3.51.4"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Protein\u2013DNA interactions often take part in various crucial processes, which are essential for cellular function. The identification of DNA-binding sites in proteins is important for understanding the molecular mechanisms of protein\u2013DNA interaction. Thus, we have developed an improved method to predict DNA-binding sites by integrating structural alignment algorithm and support vector machine\u2013based methods.<\/jats:p><jats:p>Results: Evaluated on a new non-redundant protein set with 224 chains, the method has 80.7% sensitivity and 82.9% specificity in the 5-fold cross-validation test. In addition, it predicts DNA-binding sites with 85.1% sensitivity and 85.3% specificity when tested on a dataset with 62 protein\u2013DNA complexes. Compared with a recently published method, BindN+, our method predicts DNA-binding sites with a 7% better area under the receiver operating characteristic curve value when tested on the same dataset. Many important problems in cell biology require the dense non-linear interactions between functional modules be considered. Thus, our prediction method will be useful in detecting such complex interactions.<\/jats:p><jats:p>Availability: The PreDNA webserver is freely available at: http:\/\/202.207.14.178\/predna\/index.aspx<\/jats:p><jats:p>Contact: \u00a0qzli@imu.edu.cn<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt029","type":"journal-article","created":{"date-parts":[[2013,1,19]],"date-time":"2013-01-19T04:00:52Z","timestamp":1358568052000},"page":"678-685","source":"Crossref","is-referenced-by-count":42,"title":["PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information"],"prefix":"10.1093","volume":"29","author":[{"given":"Tao","family":"Li","sequence":"first","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian-Zhong","family":"Li","sequence":"additional","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuai","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guo-Liang","family":"Fan","sequence":"additional","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong-Chun","family":"Zuo","sequence":"additional","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"},{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Peng","sequence":"additional","affiliation":[{"name":"1 Laboratory of Theoretical Biophysics, School of Physical Sciences and Technology, 2College of Computer Science and 3The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot, 010021, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,17]]},"reference":[{"key":"2023012810285622200_btt029-B1","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","article-title":"Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information","volume":"20","author":"Ahmad","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012810285622200_btt029-B2","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2105-6-33","article-title":"PSSM-based prediction of DNA binding sites in proteins","volume":"6","author":"Ahmad","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012810285622200_btt029-B3","article-title":"Methylation and uracil interference assays for analysis of protein-DNA interactions","author":"Baldwin","year":"2001","journal-title":"Curr. 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