{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:21:54Z","timestamp":1764688914895},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Computational modeling of protein\u2013DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein\u2013DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.<\/jats:p>\n               <jats:p>Results: We demonstrated the performance of this new potential in TF\u2013DNA binding affinity prediction, discrimination of native protein\u2013DNA complex from decoy structures, and most importantly in rigid TF\u2013DNA docking. The rigid TF\u2013DNA docking with the new orientation potential, on a benchmark of 38 complexes, successfully predicts 42% of the cases with root mean square deviations lower than 1 \u00c5 and 55% of the cases with root mean square deviations lower than 3 \u00c5. The results suggest that docking with this new orientation-dependent, coarse-grained statistical potential can achieve high-docking accuracy and can serve as a crucial first step in multi-stage flexible protein\u2013DNA docking.<\/jats:p>\n               <jats:p>Availability and implementation: The new potential is available at http:\/\/bioinfozen.uncc.edu\/Protein_DNA_orientation_potential.tar.<\/jats:p>\n               <jats:p>Contact: \u00a0jguo4@uncc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts699","type":"journal-article","created":{"date-parts":[[2012,12,8]],"date-time":"2012-12-08T08:17:38Z","timestamp":1354954658000},"page":"322-330","source":"Crossref","is-referenced-by-count":15,"title":["A knowledge-based orientation potential for transcription factor-DNA docking"],"prefix":"10.1093","volume":"29","author":[{"given":"Takako","family":"Takeda","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosario I.","family":"Corona","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun-tao","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,12,5]]},"reference":[{"key":"2023012810230171500_bts699-B1","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1186\/1471-2105-9-436","article-title":"Prediction of TF target sites based on atomistic models of protein-DNA complexes","volume":"9","author":"Angarica","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012810230171500_bts699-B2","doi-asserted-by":"crossref","first-page":"e73","DOI":"10.1093\/nar\/gkp242","article-title":"Assessment of the optimization of affinity and specificity at protein-DNA interfaces","volume":"37","author":"Ashworth","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012810230171500_bts699-B3","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.sbi.2007.03.004","article-title":"Multiscale modeling of biomolecular systems: in serial and in parallel","volume":"17","author":"Ayton","year":"2007","journal-title":"Curr. 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