{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T18:16:28Z","timestamp":1772907388982,"version":"3.50.1"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100006952","name":"Louisiana Board of Regents","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006952","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Board of Regents Support Fund LEQSF","award":["(2016-19)-RD-B-07"],"award-info":[{"award-number":["(2016-19)-RD-B-07"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Identification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Based on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several state-of-the-art approaches. Furthermore, when tested on recently designed two independent test datasets, StackDPPred outperforms existing approaches consistently. The proposed StackDPPred can be used for effective prediction of DNA-binding proteins from sequence alone.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Online server is at http:\/\/bmll.cs.uno.edu\/add and code-data is at http:\/\/cs.uno.edu\/\u223ctamjid\/Software\/StackDPPred\/code_data.zip.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty653","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T10:12:53Z","timestamp":1531995173000},"page":"433-441","source":"Crossref","is-referenced-by-count":121,"title":["StackDPPred: a stacking based prediction of DNA-binding protein from sequence"],"prefix":"10.1093","volume":"35","author":[{"given":"Avdesh","family":"Mishra","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of New Orleans, New Orleans, LA, USA"}]},{"given":"Pujan","family":"Pokhrel","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of New Orleans, New Orleans, LA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0110-2194","authenticated-orcid":false,"given":"Md Tamjidul","family":"Hoque","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of New Orleans, New Orleans, LA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2023013107242427300_bty653-B1","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.jmb.2004.05.058","article-title":"Moment-based prediction of DNA-binding proteins","volume":"341","author":"Ahmad","year":"2004","journal-title":"J. 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