{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T20:25:06Z","timestamp":1779135906664,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Template-based prediction of DNA binding proteins requires not only structural similarity between target and template structures but also prediction of binding affinity between the target and DNA to ensure binding. Here, we propose to predict protein\u2013DNA binding affinity by introducing a new volume-fraction correction to a statistical energy function based on a distance-scaled, finite, ideal-gas reference (DFIRE) state.<\/jats:p>\n               <jats:p>Results: We showed that this energy function together with the structural alignment program TM-align achieves the Matthews correlation coefficient (MCC) of 0.76 with an accuracy of 98%, a precision of 93% and a sensitivity of 64%, for predicting DNA binding proteins in a benchmark of 179 DNA binding proteins and 3797 non-binding proteins. The MCC value is substantially higher than the best MCC value of 0.69 given by previous methods. Application of this method to 2235 structural genomics targets uncovered 37 as DNA binding proteins, 27 (73%) of which are putatively DNA binding and only 1 protein whose annotated functions do not contain DNA binding, while the remaining proteins have unknown function. The method provides a highly accurate and sensitive technique for structure-based prediction of DNA binding proteins.<\/jats:p>\n               <jats:p>Availability: The method is implemented as a part of the Structure-based function-Prediction On-line Tools (SPOT) package available at http:\/\/sparks.informatics.iupui.edu\/spot<\/jats:p>\n               <jats:p>Contact: \u00a0yqzhou@iupui.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq295","type":"journal-article","created":{"date-parts":[[2010,6,5]],"date-time":"2010-06-05T02:21:06Z","timestamp":1275704466000},"page":"1857-1863","source":"Crossref","is-referenced-by-count":83,"title":["Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function"],"prefix":"10.1093","volume":"26","author":[{"given":"Huiying","family":"Zhao","sequence":"first","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuedong","family":"Yang","sequence":"additional","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaoqi","family":"Zhou","sequence":"additional","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,6,4]]},"reference":[{"key":"2023012507585712500_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":"2023012507585712500_B2","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":"2023012507585712500_B3","doi-asserted-by":"crossref","first-page":"6486","DOI":"10.1093\/nar\/gki949","article-title":"Kernel-based machine learning protocol for predicting DNA-binding proteins","volume":"33","author":"Bhardwaj","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012507585712500_B4","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1038\/80697","article-title":"An overview of structural genomics","volume":"7","author":"Burley","year":"2000","journal-title":"Nat. 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