{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T18:22:02Z","timestamp":1742926922445,"version":"3.40.3"},"publisher-location":"Singapore","reference-count":37,"publisher":"Springer Singapore","isbn-type":[{"type":"print","value":"9789811536069"},{"type":"electronic","value":"9789811536076"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-981-15-3607-6_30","type":"book-chapter","created":{"date-parts":[[2020,5,22]],"date-time":"2020-05-22T11:03:09Z","timestamp":1590145389000},"page":"371-383","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Prediction of DNA-Binding Protein from Profile-Based Hidden Markov Model Feature"],"prefix":"10.1007","author":[{"given":"Rianon","family":"Zaman","sequence":"first","affiliation":[]},{"given":"Khan Raqib","family":"Mahmud","sequence":"additional","affiliation":[]},{"given":"Abul Kalam","family":"Al Azad","sequence":"additional","affiliation":[]},{"given":"Md.","family":"Asifuzzaman Jishan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,5,23]]},"reference":[{"key":"30_CR1","unstructured":"Berman HM, Thornton JM, Luscombe NM1, Austin SE (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1"},{"key":"30_CR2","doi-asserted-by":"crossref","unstructured":"Bairoch A, Apweiler R (1997) The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucl Acids Res 25(1):31","DOI":"10.1093\/nar\/25.1.31"},{"key":"30_CR3","doi-asserted-by":"crossref","unstructured":"Niu XH et al (2014) Predicting DNA binding proteins using support vector machine with hybrid fractal features. J Theor BioI 343:186\u2013192","DOI":"10.1016\/j.jtbi.2013.10.009"},{"key":"30_CR4","doi-asserted-by":"crossref","unstructured":"Zhao H et al (2014) Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome. PLoS One 9(5):e96694","DOI":"10.1371\/journal.pone.0096694"},{"key":"30_CR5","doi-asserted-by":"crossref","unstructured":"Zhang Y et al (2014) NewDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation. Comput Bioi Chem 52:51\u201359","DOI":"10.1016\/j.compbiolchem.2014.09.002"},{"key":"30_CR6","doi-asserted-by":"crossref","unstructured":"Wang W et al (2014) Identification of single-stranded and double-stranded DNA binding proteins based on protein structure. BMC Bioinform 15(Suppl 12):S4","DOI":"10.1186\/1471-2105-15-S12-S4"},{"key":"30_CR7","doi-asserted-by":"crossref","unstructured":"Stawiski EW et al (2013) Annotating nucleic acid-binding function based on protein structure. Mol Biol 326:1065\u20131079","DOI":"10.1016\/S0022-2836(03)00031-7"},{"key":"30_CR8","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.jmb.2004.05.058","volume":"341","author":"S Ahmad","year":"2004","unstructured":"Ahmad S, Sarai A (2004) Moment-based prediction of DNA-binding proteins. J Mol Biol 341:65\u201371","journal-title":"J Mol Biol"},{"key":"30_CR9","doi-asserted-by":"crossref","unstructured":"Nimrod G et al (2009) Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol 387:1040\u20131053","DOI":"10.1016\/j.jmb.2009.02.023"},{"key":"30_CR10","doi-asserted-by":"crossref","unstructured":"Zen A et al (2009) Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains. Bioinformatics 25:1876\u20131883","DOI":"10.1093\/bioinformatics\/btp339"},{"key":"30_CR11","unstructured":"Luthy R, Eisenberg D, Bowie J (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016):164\u2013170"},{"key":"30_CR12","unstructured":"Luthy R, Eisenberg D, Bowie J (2008) A knowledge-based method for the prediction of DNA-protein interactions. Nucl Acids Res 36(15):3978\u20133992"},{"key":"30_CR13","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","volume":"20","author":"A Sarai","year":"2004","unstructured":"Sarai A, Ahmad S, Gromiha MM (2004) Analysis and prediction of dnabinding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20:477\u2013486","journal-title":"Bioinformatics"},{"issue":"2","key":"30_CR14","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/s00726-008-0044-7","volume":"36","author":"A Lumini","year":"2009","unstructured":"Lumini A, Nanni L (2009) An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins. Amino Acids 36(2):167\u2013175","journal-title":"Amino Acids"},{"key":"30_CR15","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1038\/12873","volume":"17","author":"HF Jorgensen","year":"1999","unstructured":"Jorgensen HF, Kallipolitis BH, Clark BF, Nordhoff E, Krogsdam AM (1999) Rapid identification of DNA-binding proteins by mass spectrometry. Nat Biotechnol 17:884\u2013888","journal-title":"Nat Biotechnol"},{"key":"30_CR16","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1080\/07391102.2009.10507281","volume":"26","author":"PN Suganthan","year":"2009","unstructured":"Suganthan PN, Kumar KK, Pugalenthi G (2009) DNA-prot: identification of DNA binding proteins from protein sequence information using random forest. J Biomol Struct Dyn 26:679\u2013686","journal-title":"J Biomol Struct Dyn"},{"key":"30_CR17","doi-asserted-by":"crossref","unstructured":"Lumini A, Nanni L (2008) Combing ontologies and dipeptide composition for predicting DNA-binding proteins. Amino Acids 34:635\u2013641","DOI":"10.1007\/s00726-007-0016-3"},{"key":"30_CR18","doi-asserted-by":"publisher","first-page":"3149","DOI":"10.1093\/nar\/gkq061","volume":"38","author":"H Lu","year":"2010","unstructured":"Lu H, Langlois RE (2010) Boosting the prediction and understanding of DNA-binding domains from sequence. Nucl Acids Res 38:3149\u20133158","journal-title":"Nucl Acids Res"},{"key":"30_CR19","first-page":"6486","volume":"33","author":"G Zhao","year":"2009","unstructured":"Zhao G, Lu H, Bhardwaj N, Langlois RE (2009) Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucl Acids 33:6486\u20136493","journal-title":"Nucl Acids"},{"key":"30_CR20","first-page":"6486","volume":"240","author":"Y Cai","year":"2006","unstructured":"Cai Y, Shi T, Li Y, Yu X, Cao J (2006) Predicting rRNA-, RNA-, and dnabinding proteins from primary structure with support vector machines. J Theor Biol 240:6486\u20136493","journal-title":"J Theor Biol"},{"key":"30_CR21","doi-asserted-by":"crossref","unstructured":"Akutsu T, Brown J (2009) Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. BMC Bioinforma 10(1)","DOI":"10.1186\/1471-2105-10-25"},{"issue":"5","key":"30_CR22","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1093\/bioinformatics\/btq019","volume":"26","author":"A Szilgyi","year":"2010","unstructured":"Szilgyi A, Leslie C, Ben-Tal N, Nimrod G, Schushan M (2010) iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics 26(5):692\u2013693","journal-title":"Bioinformatics"},{"key":"30_CR23","doi-asserted-by":"crossref","unstructured":"Kumar M, Gromiha MM, Raghava GPS (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinform 8(1):463","DOI":"10.1186\/1471-2105-8-463"},{"key":"30_CR24","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/S1570-9639(03)00112-2","volume":"1648","author":"SL Lin","year":"2003","unstructured":"Lin SL, Cai YD (2003) Support vector machines for predicting rRNA, RNA, and DNA-binding proteins from amino acid sequence. Biochim Biophys Acta 1648:127\u2013133","journal-title":"Biochim Biophys Acta"},{"key":"30_CR25","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/1471-2105-14-90","volume":"14","author":"H Li","year":"2013","unstructured":"Li H, Zou C, Gong J (2013) An improved sequence based prediction protocol for DNA-binding proteins using svm and comprehensive feature analysis. BMC Bioinform 14:90","journal-title":"BMC Bioinform"},{"key":"30_CR26","doi-asserted-by":"publisher","first-page":"15479","DOI":"10.1038\/srep15479","volume":"5","author":"X Wang","year":"2015","unstructured":"Wang X, Liu B, Wang S (2015) DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation. Sci Rep 5:15479","journal-title":"Sci Rep"},{"issue":"4","key":"30_CR27","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1109\/TNB.2016.2555951","volume":"15","author":"Q Dong","year":"2016","unstructured":"Dong Q, Li S, Liu X, Liu B, Wang S (2016) Identification of DNA-binding proteins by combining auto-cross covariance transformation and ensemble learning. IEEE Trans Nanobiosci 15(4):328\u2013334","journal-title":"IEEE Trans Nanobiosci"},{"issue":"1","key":"30_CR28","doi-asserted-by":"publisher","first-page":"e86703","DOI":"10.1371\/journal.pone.0086703","volume":"9","author":"W Lou","year":"2014","unstructured":"Lou W, Wang X, Chen F, Chen Y, Jiang B, Zhang H (2014) Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and gaussian naive bayes. PLoS One 9(1):e86703","journal-title":"PLoS One"},{"key":"30_CR29","doi-asserted-by":"crossref","unstructured":"Qin J, Liu X, Jiang Y, Ke C, Zou Q, Lin C, Zou Y (2012) Hierarchical classification of protein folds using a novel ensemble classifier. PLoS One 8(2)","DOI":"10.1371\/journal.pone.0056499"},{"issue":"4","key":"30_CR30","first-page":"467","volume":"18","author":"PV de Souza","year":"1992","unstructured":"de Souza PV, Lai JC, Mercer RL, Brown PF, Della Pietra VJ (1992) Class-based n-gram models of natural language. Comput Linguist 18(4):467\u2013479","journal-title":"Comput Linguist"},{"key":"30_CR31","unstructured":"Gong XJ, Xu JH, Lee HS, Qu YH, Yu H (2017) On the prediction of DNA-binding proteins only from primary sequences: a deep learning approach. PLOS One"},{"key":"30_CR32","doi-asserted-by":"crossref","unstructured":"Zaman R (2017) Hmmbinder: DNA-binding protein prediction using hmm profile based features. Biomed Res Int 2017:10","DOI":"10.1155\/2017\/4590609"},{"key":"30_CR33","unstructured":"Dondoshansky I, Wolf Y (2002) Blastclust (NCBI software development toolkit). NCBI, Bethesda, Md"},{"issue":"2","key":"30_CR34","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1038\/nmeth.1818","volume":"9","author":"M Remmert","year":"2012","unstructured":"Remmert M, Biegert A, Hauser A, S\u00f6ding J (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat methods 9(2):173\u2013175","journal-title":"Nat methods"},{"key":"30_CR35","doi-asserted-by":"crossref","unstructured":"Kuchibhatla DB, Sherman WA, Chung BY, Cook S, Schneider G, Eisenhaber B, Karlin DG (2014) Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently orphan viral proteins. J Virol 88(1):10\u201320","DOI":"10.1128\/JVI.02595-13"},{"key":"30_CR36","unstructured":"UniProt Consortium (2017) Uniprot: the universal protein knowledge base. Nucl Acids Res 45(D1):D158\u2013D169"},{"key":"30_CR37","unstructured":"Lyons J, Paliwal KK, Sharma A, Dehzangi A (2014) A tri-gram based feature extraction technique using linear probabilities of position specific scoring matrix for protein fold recognition. IEEE Trans NanoBiosci 13(1):44\u201350"}],"container-title":["Algorithms for Intelligent Systems","Proceedings of International Joint Conference on Computational Intelligence"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-981-15-3607-6_30","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T16:32:40Z","timestamp":1601310760000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-981-15-3607-6_30"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9789811536069","9789811536076"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/978-981-15-3607-6_30","relation":{},"ISSN":["2524-7565","2524-7573"],"issn-type":[{"type":"print","value":"2524-7565"},{"type":"electronic","value":"2524-7573"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"23 May 2020","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}