{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T05:52:45Z","timestamp":1725861165969},"publisher-location":"Cham","reference-count":27,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319422930"},{"type":"electronic","value":"9783319422947"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-3-319-42294-7_79","type":"book-chapter","created":{"date-parts":[[2016,7,11]],"date-time":"2016-07-11T15:00:47Z","timestamp":1468249247000},"page":"888-894","source":"Crossref","is-referenced-by-count":0,"title":["Computational Analysis of Similar Protein-DNA Complexes from Different Organisms to Understand Organism Specific Recognition"],"prefix":"10.1007","author":[{"given":"R.","family":"Nagarajan","sequence":"first","affiliation":[]},{"given":"M. Michael","family":"Gromiha","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,7,12]]},"reference":[{"key":"79_CR1","doi-asserted-by":"crossref","first-page":"4741","DOI":"10.1021\/jp076432e","volume":"112","author":"AG Cherstvy","year":"2008","unstructured":"Cherstvy, A.G., Kolomeisky, A.B., Kornyshev, A.A.: Protein DNA interactions: reaching and recognizing the targets. J. Phys. Chem. B 112, 4741\u20134750 (2008)","journal-title":"J. Phys. Chem. B"},{"issue":"8","key":"79_CR2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.tibs.2011.04.006","volume":"36","author":"M Fuxreiter","year":"2011","unstructured":"Fuxreiter, M., Simon, I., Bondos, S.: Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem. Sci. 36(8), 15\u201323 (2011)","journal-title":"Trends Biochem. Sci."},{"issue":"3","key":"79_CR3","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1021\/ci1003703","volume":"51","author":"MM Gromiha","year":"2011","unstructured":"Gromiha, M.M., Fukui, K.: Scoring function based approach for locating binding sites and understanding the recognition mechanism of protein-DNA complexes. J. Chem. Inf. Model. 51(3), 7\u20139 (2011)","journal-title":"J. Chem. Inf. Model."},{"key":"79_CR4","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1021\/bi982362d","volume":"38","author":"K Nadassy","year":"1999","unstructured":"Nadassy, K., Wodak, S.J., Janin, J.: Structural features of protein-nucleic acid recognition sites. Biochemistry 38, 1999\u20132017 (1999)","journal-title":"Biochemistry"},{"issue":"1","key":"79_CR5","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.str.2003.11.022","volume":"12","author":"G Paillard","year":"2004","unstructured":"Paillard, G., Lavery, R.: Analyzing protein-DNA recognition mechanisms. Structure 12(1), 11\u201322 (2004)","journal-title":"Structure"},{"key":"79_CR6","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/gku1403","volume":"43","author":"PW Rose","year":"2015","unstructured":"Rose, P.W., Prli\u0107, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D., Woo, J., Young, J., Zardecki, C., Berman, H.M., Bourne, P.E., Burley, S.K.: The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 43, 45\u201356 (2015)","journal-title":"Nucleic Acids Res."},{"key":"79_CR7","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","volume":"20","author":"S Ahmad","year":"2004","unstructured":"Ahmad, S., Gromiha, M.M., Sarai, A.: Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20, 477\u2013486 (2004)","journal-title":"Bioinformatics"},{"key":"79_CR8","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1093\/nar\/gkm008","volume":"35","author":"H Tjong","year":"2007","unstructured":"Tjong, H., Zhou, H.-X.: DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acid Res. 35, 1465\u20131477 (2007)","journal-title":"Nucleic Acid Res."},{"key":"79_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1007\/978-3-642-14922-1_78","volume-title":"Advanced Intelligent Computing Theories and Applications","author":"M Gromiha","year":"2010","unstructured":"Gromiha, M., Selvaraj, S., Jayaram, B., Fukui, K.: Identification and analysis of binding site residues in protein complexes: energy based approach. In: Huang, D.-S., Zhao, Z., Bevilacqua, V., Figueroa, J.C. (eds.) ICIC 2010. LNCS, vol. 6215, pp. 626\u2013633. Springer, Heidelberg (2010)"},{"key":"79_CR10","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1146\/annurev.biophys.34.040204.144537","volume":"34","author":"A Sarai","year":"2005","unstructured":"Sarai, A., Kono, H.: Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct. 34, 379\u2013398 (2005)","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"79_CR11","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/329263a0","volume":"329","author":"ME Hogan","year":"1987","unstructured":"Hogan, M.E., Austin, R.H.: Importance of DNA stiffness in protein-DNA binding specificity. Nature 329, 263\u2013266 (1987)","journal-title":"Nature"},{"key":"79_CR12","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/S0301-4622(97)00088-4","volume":"69","author":"MM Gromiha","year":"1987","unstructured":"Gromiha, M.M., Munteanu, M.G., Simon, I., Pongor, S.: The role of DNA bending in Cro protein-DNA interactions. Biophys. Chem. 69, 153\u2013160 (1987)","journal-title":"Biophys. Chem."},{"key":"79_CR13","doi-asserted-by":"crossref","first-page":"11163","DOI":"10.1073\/pnas.95.19.11163","volume":"95","author":"WK Olson","year":"1998","unstructured":"Olson, W.K., Gorin, A.A., Lu, X.J., Hock, L.M., Zhurkin, V.B.: DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA 95, 11163\u201311168 (1998)","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"79_CR14","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.jbiotec.2004.12.016","volume":"117","author":"MM Gromiha","year":"2005","unstructured":"Gromiha, M.M.: Influence of DNA stiffness in protein-DNA recognition. J. Biotechnol. 117, 137\u2013145 (2005)","journal-title":"J. Biotechnol."},{"key":"79_CR15","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1006\/jmbi.1998.1660","volume":"277","author":"Y Mandel-Gutfreund","year":"1998","unstructured":"Mandel-Gutfreund, Y., Margalit, H., Jernigan, R.L., Zhurkin, V.B.: A role for CH\u00b7\u00b7\u00b7O interactions in protein-DNA recognition. J. Mol. Biol. 277, 1129\u20131140 (1998)","journal-title":"J. Mol. Biol."},{"key":"79_CR16","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1006\/jmbi.1999.2659","volume":"287","author":"S Jones","year":"1999","unstructured":"Jones, S., van Heyningen, P., Berman, H.M., Thornton, J.M.: Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287, 877\u2013896 (1999)","journal-title":"J. Mol. Biol."},{"key":"79_CR17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/jcc.10009","volume":"23","author":"B Jayaram","year":"2002","unstructured":"Jayaram, B., McConnell, K., Dixit, S.B., Das, A., Beveridge, D.L.: Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. J. Comput. Chem. 23, 1\u201314 (2002)","journal-title":"J. Comput. Chem."},{"issue":"337","key":"79_CR18","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.jmb.2004.01.033","volume":"2004","author":"MM Gromiha","year":"2004","unstructured":"Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A.: Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J. Mol. Biol. 2004(337), 285\u2013294 (2004)","journal-title":"J. Mol. Biol."},{"key":"79_CR19","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1016\/j.str.2006.06.018","volume":"14","author":"P Prabakaran","year":"2006","unstructured":"Prabakaran, P., Siebers, J.G., Ahmad, S., Gromiha, M.M., Singarayan, M.G., Sarai, A.: Classification of protein-DNA complexes based on structural descriptors. Structure 14, 1355\u20131367 (2006)","journal-title":"Structure"},{"key":"79_CR20","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.polymer.2003.10.069","volume":"45","author":"MM Gromiha","year":"2004","unstructured":"Gromiha, M.M., Santhosh, C., Suwa, W.: Influence of cation-pi interactions in protein-DNA complexes. Polymer 45, 633\u2013639 (2004)","journal-title":"Polymer"},{"key":"79_CR21","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1002\/(SICI)1097-0134(19990401)35:1<114::AID-PROT11>3.0.CO;2-T","volume":"35","author":"H Kono","year":"1999","unstructured":"Kono, H., Sarai, A.: Structure-based prediction of DNA target sites by regulatory proteins. Proteins 35, 114\u2013131 (1999)","journal-title":"Proteins"},{"key":"79_CR22","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1093\/nar\/gkl1103","volume":"35","author":"JE Donald","year":"2007","unstructured":"Donald, J.E., Chen, W.W., Shakhnovich, E.I.: Energetics of protein-DNA interactions. Nucleic Acids Res. 35, 1039\u20131047 (2007)","journal-title":"Nucleic Acids Res."},{"key":"79_CR23","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/B978-0-12-411637-5.00003-2","volume":"91","author":"MM Gromiha","year":"2013","unstructured":"Gromiha, M.M., Nagarajan, R.: Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. Adv. Protein Chem. Struct. Biol. 91, 65\u201399 (2013)","journal-title":"Adv. Protein Chem. Struct. Biol."},{"key":"79_CR24","doi-asserted-by":"crossref","first-page":"7606","DOI":"10.1093\/nar\/gkt544","volume":"41","author":"R Nagarajan","year":"2013","unstructured":"Nagarajan, R., Ahmad, S., Gromiha, M.M.: Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. Nucleic Acids Res. 41, 7606\u20137614 (2013)","journal-title":"Nucleic Acids Res."},{"key":"79_CR25","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13062-015-0039-8","volume":"10","author":"R Nagarajan","year":"2015","unstructured":"Nagarajan, R., Chothani, S.P., Ramakrishnan, C., Sekijima, M., Gromiha, M.M.: Structure based approach for understanding organism specific recognition of protein-RNA complexes. Biol. Direct 10, 8 (2015)","journal-title":"Biol. Direct"},{"key":"79_CR26","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1039\/b904161n","volume":"5","author":"MM Gromiha","year":"2009","unstructured":"Gromiha, M.M., Yokota, K., Fukui, K.: Energy based approach for understanding the recognition mechanism in protein-protein complexes. Mol. BioSyst. 5, 1779\u20131786 (2009)","journal-title":"Mol. BioSyst."},{"key":"79_CR27","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1093\/bioinformatics\/19.1.163","volume":"19","author":"F Glaser","year":"2003","unstructured":"Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor, D., Martz, E., Ben-Tal, N.: ConSurf: identification of functional regions in proteins by surface mapping of phylogenetic information. Bioinformatics 19, 163\u2013164 (2003)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Intelligent Computing Theories and Application"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-42294-7_79","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T18:12:00Z","timestamp":1498327920000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-42294-7_79"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319422930","9783319422947"],"references-count":27,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-42294-7_79","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2016]]}}}