{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T18:51:44Z","timestamp":1770835904161,"version":"3.50.1"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T00:00:00Z","timestamp":1541376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Because DNA-binding proteins (DNA-BPs) play a vital role in all aspects of genetic activity, the development of reliable and efficient systems for automatic DNA-BP classification is becoming a crucial proteomic technology. Key to this technology is the discovery of powerful protein representations and feature extraction methods. The goal of this article is to develop experimentally a system for automatic DNA-BP classification by comparing and combining different descriptors taken from different types of protein representations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The descriptors we evaluate include those starting from the position-specific scoring matrix (PSSM) of proteins, those derived from the amino-acid sequence (AAS), various matrix representations of proteins and features taken from the three-dimensional tertiary structure of proteins. We also introduce some new variants of protein descriptors. Each descriptor is used to train a separate support vector machine (SVM), and results are combined by sum rule. Our final system obtains state-or-the-art results on three benchmark DNA-BP datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The MATLAB code for replicating the experiments presented in this paper is available at https:\/\/github.com\/LorisNanni.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty912","type":"journal-article","created":{"date-parts":[[2018,11,1]],"date-time":"2018-11-01T06:59:14Z","timestamp":1541055554000},"page":"1844-1851","source":"Crossref","is-referenced-by-count":16,"title":["Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins"],"prefix":"10.1093","volume":"35","author":[{"given":"Loris","family":"Nanni","sequence":"first","affiliation":[{"name":"Department of Information Engineering, University of Padova, Padova, Italy"}]},{"given":"Sheryl","family":"Brahnam","sequence":"additional","affiliation":[{"name":"Department of Computer Information Systems, Missouri State University, Springfield, MO, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,11,5]]},"reference":[{"key":"2023012713072156100_bty912-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012713072156100_bty912-B2","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1093\/bioinformatics\/btt072","article-title":"Propy: a tool to generate various modes of Chou\u2019s PseAAC","volume":"29","author":"Cao","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012713072156100_bty912-B3","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1109\/TPAMI.2009.155","article-title":"WLD: a robust local image descriptor","volume":"32","author":"Chen","year":"2010","journal-title":"IEEE Trans. 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