Chu W.-Y.Huang Y.-F.Huang C.-C.Cheng Y.-S.Huang C.-K.CHIEN-KANG HUANGYEN-JEN OYANG2019-07-222019-07-22200903051048https://scholars.lib.ntu.edu.tw/handle/123456789/414373This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites: http://protedna.csbb.ntu.edu.tw/ http://protedna.csbb.ntu.edu.tw/ http://bio222.esoe.ntu.edu.tw/ProteDNA.journal article10.1093/nar/gkp449https://www.scopus.com/inward/record.uri?eid=2-s2.0-67849090551&doi=10.1093%2fnar%2fgkp449&partnerID=40&md5=7f509a4cfc7134eedbc8609709f1dfe12-s2.0-67849090551https://www.scopus.com/inward/record.uri?eid=2-s2.0-67849090551&doi=10.1093%2fnar%2fgkp449&partnerID=40&md5=7f509a4cfc7134eedbc8609709f1dfe1