{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T13:37:54Z","timestamp":1762781874208},"reference-count":69,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2015,1,10]],"date-time":"2015-01-10T00:00:00Z","timestamp":1420848000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2015,3]]},"DOI":"10.1007\/s10822-014-9828-x","type":"journal-article","created":{"date-parts":[[2015,1,9]],"date-time":"2015-01-09T12:43:49Z","timestamp":1420807429000},"page":"283-295","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Role of indirect readout mechanism in TATA box binding protein\u2013DNA interaction"],"prefix":"10.1007","volume":"29","author":[{"given":"Manas","family":"Mondal","sequence":"first","affiliation":[]},{"given":"Devapriya","family":"Choudhury","sequence":"additional","affiliation":[]},{"given":"Jaydeb","family":"Chakrabarti","sequence":"additional","affiliation":[]},{"given":"Dhananjay","family":"Bhattacharyya","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,1,10]]},"reference":[{"issue":"2","key":"9828_CR1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.sbi.2005.01.018","volume":"15","author":"C Deremble","year":"2005","unstructured":"Deremble C, Lavery R (2005) Macromollecullar recognition. Curr Opin Struct Biol 15(2):171\u2013175. doi: 10.1016\/j.sbi.2005.01.018","journal-title":"Curr Opin Struct Biol"},{"key":"9828_CR2","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 (2005) Protein\u2013DNA recognition patterns and predictions. Annu Rev Biophys Biomol Struct 34:379\u2013398. doi: 10.1146\/annurev.biophys.34.040202.144537","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"1339","key":"9828_CR3","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1098\/rstb.1996.0048","volume":"351","author":"D Rhodes","year":"1996","unstructured":"Rhodes D, Schwabe JWR, Chapman L, Fairall L (1996) Towards an understanding of protein\u2013DNA recognition. Philos Trans R Soc Lond Ser B 351(1339):501\u2013509. doi: 10.1098\/rstb.1996.0048","journal-title":"Philos Trans R Soc Lond Ser B"},{"issue":"1","key":"9828_CR4","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.str.2003.11.022","volume":"12","author":"G Paillard","year":"2004","unstructured":"Paillard G, Lavery R (2004) Analyzing protein\u2013DNA recognition mechanisms. Structure\u00a012(1):113\u2013122. doi: 10.1016\/j.str.2003.11.022","journal-title":"Structure"},{"key":"9828_CR5","first-page":"9","volume":"27","author":"E Fischer","year":"1894","unstructured":"Fischer E (1894) Einfluss der configuration auf die wirkung der enzyme. Ber Dtsch Chem Ges 27:9","journal-title":"Ber Dtsch Chem Ges"},{"issue":"2","key":"9828_CR6","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.jmb.2004.01.033","volume":"337","author":"MM Gromiha","year":"2004","unstructured":"Gromiha MM, Siebers JG, Selvaraj S, Kono H, Sarai A (2004) Intermolecular and intramolecular readout mechanisms in protein\u2013DNA recognition. J Mol Biol 337(2):285\u2013294. doi: 10.1016\/j.jmb.2004.01.033","journal-title":"J Mol Biol"},{"key":"9828_CR7","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.gene.2005.07.022","volume":"364","author":"MM Gromiha","year":"2005","unstructured":"Gromiha MM, Slebcrs JG, Selvaraj S, Kono H, Sarai A (2005) Role of inter and intramolecular interactions in protein\u2013DNA recognition. Gene 364:108\u2013113. doi: 10.1016\/j.gene.2005.07.022","journal-title":"Gene"},{"issue":"2","key":"9828_CR8","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.44.2.98","volume":"44","author":"DE Koshland","year":"1958","unstructured":"Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44(2):98\u2013104. doi: 10.1073\/pnas.44.2.98","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"9828_CR9","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/protein\/12.9.713","volume":"12","author":"BY Ma","year":"1999","unstructured":"Ma BY, Kumar S, Tsai CJ, Nussinov R (1999) Folding funnels and binding mechanisms. Protein Eng 12(9):713\u2013720. doi: 10.1093\/protein\/12.9.713","journal-title":"Protein Eng"},{"issue":"1","key":"9828_CR10","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1002\/prot.340230111","volume":"23","author":"JM Troyer","year":"1995","unstructured":"Troyer JM, Cohen FE (1995) Protein conformational landscapes\u2014energy minimization and clustering of a long molecular-dynamics trajectory. Proteins Struct Funct Genet 23(1):97\u2013110. doi: 10.1002\/prot.340230111","journal-title":"Proteins Struct Funct Genet"},{"issue":"5038","key":"9828_CR11","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1126\/science.1749933","volume":"254","author":"H Frauenfelder","year":"1991","unstructured":"Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254(5038):1598\u20131603. doi: 10.1126\/science.1749933","journal-title":"Science"},{"issue":"11","key":"9828_CR12","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nchembio.232","volume":"5","author":"DD Boehr","year":"2009","unstructured":"Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789\u2013796. doi: 10.1038\/nchembio1209-954d","journal-title":"Nat Chem Biol"},{"issue":"1","key":"9828_CR13","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1110\/ps.9.1.10","volume":"9","author":"S Kumar","year":"2000","unstructured":"Kumar S, Ma BY, Tsai CJ, Sinha N, Nussinov R (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9(1):10\u201319. doi: 10.1110\/ps.9.1.10","journal-title":"Protein Sci"},{"issue":"12","key":"9828_CR14","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1016\/j.str.2004.09.014","volume":"12","author":"R Grunberg","year":"2004","unstructured":"Grunberg R, Leckner J, Nilges M (2004) Complementarity of structure ensembles in protein\u2013protein binding. Structure\u00a012(12):2125\u20132136. doi: 10.1016\/j.str.2004.09.014","journal-title":"Structure"},{"issue":"46","key":"9828_CR15","doi-asserted-by":"crossref","first-page":"19346","DOI":"10.1073\/pnas.0906966106","volume":"106","author":"T Wlodarski","year":"2009","unstructured":"Wlodarski T, Zagrovic B (2009) Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc Natl Acad Sci USA 106(46):19346\u201319351. doi: 10.1073\/pnas.0906966106","journal-title":"Proc Natl Acad Sci USA"},{"issue":"10","key":"9828_CR16","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.tibs.2010.04.009","volume":"35","author":"P Csermely","year":"2010","unstructured":"Csermely P, Palotai R, Nussinov R (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 35(10):539\u2013546. doi: 10.1016\/j.tibs.2010.04.009","journal-title":"Trends Biochem Sci"},{"issue":"4","key":"9828_CR17","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/0022-2836(79)90196-7","volume":"131","author":"A Klug","year":"1979","unstructured":"Klug A, Jack A, Viswamitra MA, Kennard O, Shakked Z, Steitz TA (1979) Hypothesis on a specific sequence-dependent conformation of dna and its relation to the binding of the lac-repressor protein. J Mol Biol 131(4):669\u2013680. doi: 10.1016\/0022-2836(79)90196-7","journal-title":"J Mol Biol"},{"issue":"5","key":"9828_CR18","doi-asserted-by":"crossref","first-page":"3147","DOI":"10.1529\/biophysj.104.053843","volume":"88","author":"SB Dixit","year":"2005","unstructured":"Dixit SB, Andrews DQ, Beveridge DL (2005) Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences. Biophys J 88(5):3147\u20133157. doi: 10.1529\/biophysj.104.053843","journal-title":"Biophys J"},{"issue":"2","key":"9828_CR19","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.jmb.2004.08.035","volume":"343","author":"AI Dragan","year":"2004","unstructured":"Dragan AI, Read CM, Makeyeva EN, Milgotina EI, Churchill MEA, Crane-Robinson C, Privalov PL (2004) DNA binding and bending by HMG boxes: energetic determinants of specificity. J Mol Biol 343(2):371\u2013393. doi: 10.1016\/j.jmb.2004.08.035","journal-title":"J Mol Biol"},{"issue":"26","key":"9828_CR20","doi-asserted-by":"crossref","first-page":"15163","DOI":"10.1073\/pnas.95.26.15163","volume":"95","author":"DM Crothers","year":"1998","unstructured":"Crothers DM (1998) DNA curvature and deformation in protein\u2013DNA complexes: a step in the right direction. Proc Natl Acad Sci USA 95(26):15163\u201315165. doi: 10.1073\/pnas.95.26.15163","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"9828_CR21","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1006\/jmbi.1999.2947","volume":"291","author":"NA Davis","year":"1999","unstructured":"Davis NA, Majee SS, Kahn JD (1999) TATA box DNA deformation with and without the TATA box-binding protein. J Mol Biol 291(2):249\u2013265. doi: 10.1006\/jmbi.1999.2947","journal-title":"J Mol Biol"},{"issue":"13","key":"9828_CR22","doi-asserted-by":"crossref","first-page":"4242","DOI":"10.1021\/jp810009s","volume":"113","author":"AG Cherstvy","year":"2009","unstructured":"Cherstvy AG (2009) Positively Charged Residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups. J Phys Chem B 113(13):4242\u20134247. doi: 10.1021\/jp810009s","journal-title":"J Phys Chem B"},{"issue":"4","key":"9828_CR23","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1002\/bip.10389","volume":"69","author":"M Garcia-Perez","year":"2003","unstructured":"Garcia-Perez M, Pinto M, Subirana JA (2003) Nonsequence-specific arginine interactions in the nucleosome core particle. Biopolymers 69(4):432\u2013439. doi: 10.1002\/bip.10389","journal-title":"Biopolymers"},{"issue":"5250","key":"9828_CR24","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1126\/science.271.5250.778","volume":"271","author":"MH Werner","year":"1996","unstructured":"Werner MH (1996) Intercalation, DNA kinking, and the control of transcription. Science 271(5250):778\u2013784. doi: 10.1126\/science.271.5250.778","journal-title":"Science"},{"issue":"9","key":"9828_CR25","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.tibs.2009.05.005","volume":"34","author":"PL Privalov","year":"2009","unstructured":"Privalov PL, Dragan AI, Crane-Robinson C (2009) The cost of DNA bending. Trends Biochem Sci 34(9):464\u2013470. doi: 10.1016\/j.tibs.2009.05.005","journal-title":"Trends Biochem Sci"},{"issue":"6446","key":"9828_CR26","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/365512a0","volume":"365","author":"YC Kim","year":"1993","unstructured":"Kim YC, Geiger JH, Hahn S, Sigler PB (1993) Crystal-structure of a yeast TBP TATA-box complex. Nature 365(6446):512\u2013520. doi: 10.1038\/365512a0","journal-title":"Nature"},{"issue":"9","key":"9828_CR27","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nsb0994-621","volume":"1","author":"DB Nikolov","year":"1994","unstructured":"Nikolov DB, Burley SK (1994) 2.1-Angstrom resolution refined structure of a TATA box-binding protein (TBP). Nat Struct Biol 1(9):621\u2013637. doi: 10.1038\/nsb0994-621","journal-title":"Nat Struct Biol"},{"issue":"2","key":"9828_CR28","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1016\/S0021-9258(18)48443-8","volume":"267","author":"A Osheagreenfield","year":"1992","unstructured":"Osheagreenfield A, Smale ST (1992) Roles of TATA and initiator elements in determining the start site location and direction of rna polymerase-II transcription. J Biol Chem 267(2):1391\u20131402","journal-title":"J Biol Chem"},{"issue":"4","key":"9828_CR29","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1101\/gad.4.4.636","volume":"4","author":"VL Singer","year":"1990","unstructured":"Singer VL, Wobbe CR, Struhl K (1990) A wide variety of DNA-sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev 4(4):636\u2013645. doi: 10.1101\/gad.4.4.636","journal-title":"Genes Dev"},{"issue":"19","key":"9828_CR30","doi-asserted-by":"crossref","first-page":"8606","DOI":"10.1073\/pnas.92.19.8606","volume":"92","author":"Y Wang","year":"1995","unstructured":"Wang Y, Stumph WE (1995) RNA-polymerase II\/III transcription specificity determined by TATA box orientation. Proc Natl Acad Sci USA 92(19):8606\u20138610. doi: 10.1073\/pnas.92.19.8606","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"9828_CR31","doi-asserted-by":"crossref","first-page":"3859","DOI":"10.1128\/MCB.10.8.3859","volume":"10","author":"CR Wobbe","year":"1990","unstructured":"Wobbe CR, Struhl K (1990) Yeast and human TATA-binding proteins have nearly identical DNA-sequence requirements for transcription invitro. Mol Cell Biol 10(8):3859\u20133867. doi: 10.1128\/MCB.10.8.3859","journal-title":"Mol Cell Biol"},{"issue":"6446","key":"9828_CR32","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/365520a0","volume":"365","author":"JL Kim","year":"1993","unstructured":"Kim JL, Nikolov DB, Burley SK (1993) Co-crystal structure of TBP recognizing the minor-groove of a TATA element. Nature 365(6446):520\u2013527. doi: 10.1038\/365520a0","journal-title":"Nature"},{"issue":"9","key":"9828_CR33","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nsb0994-638","volume":"1","author":"JL Kim","year":"1994","unstructured":"Kim JL, Burley SK (1994) 1.9-Angstrom resolution refined structure of TBP recognizing the minor-groove of TATAAAAG. Nat Struct Biol 1(9):638\u2013653. doi: 10.1038\/nsb0994-638","journal-title":"Nat Struct Biol"},{"issue":"10","key":"9828_CR34","doi-asserted-by":"crossref","first-page":"4862","DOI":"10.1073\/pnas.93.10.4862","volume":"93","author":"DB Nikolov","year":"1996","unstructured":"Nikolov DB, Chen H, Halay ED, Hoffmann A, Roeder RG, Burley SK (1996) Crystal structure of a human TATA box-binding protein\/TATA element complex. Proc Natl Acad Sci USA 93(10):4862\u20134867. doi: 10.1073\/pnas.93.10.4862","journal-title":"Proc Natl Acad Sci USA"},{"issue":"18","key":"9828_CR35","doi-asserted-by":"crossref","first-page":"14614","DOI":"10.1074\/jbc.M004402200","volume":"276","author":"J Wu","year":"2001","unstructured":"Wu J, Parkhurst KM, Powell RM, Brenowitz M, Parkhurst LJ (2001) DNA bends in TATA-binding protein center dot TATA complexes in solution are DNA sequence-dependent. J Biol Chem 276(18):14614\u201314622. doi: 10.1074\/jbc.M004402200","journal-title":"J Biol Chem"},{"issue":"18","key":"9828_CR36","doi-asserted-by":"crossref","first-page":"14623","DOI":"10.1074\/jbc.M004401200","volume":"276","author":"J Wu","year":"2001","unstructured":"Wu J, Parkhurst KM, Powell RM, Parkhurst LJ (2001) DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes. J Biol Chem 276(18):14623\u201314627. doi: 10.1074\/jbc.M004401200","journal-title":"J Biol Chem"},{"issue":"35","key":"9828_CR37","doi-asserted-by":"crossref","first-page":"15421","DOI":"10.1073\/pnas.1004809107","volume":"107","author":"S Geggier","year":"2010","unstructured":"Geggier S, Vologodskii A (2010) Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci USA 107(35):15421\u201315426. doi: 10.1073\/pnas.1004809107","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"9828_CR38","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1093\/nar\/gkm1125","volume":"36","author":"Q Du","year":"2008","unstructured":"Du Q, Kotlyar A, Vologodskii A (2008) Kinking the double helix by bending deformation. Nucleic Acids Res 36(4):1120\u20131128. doi: 10.1093\/nar\/gkm1125","journal-title":"Nucleic Acids Res"},{"issue":"6098","key":"9828_CR39","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1224139","volume":"337","author":"R Vafabakhsh","year":"2012","unstructured":"Vafabakhsh R, Ha T (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337(6098):1097\u20131101. doi: 10.1126\/science.1224139","journal-title":"Science"},{"issue":"8","key":"9828_CR40","doi-asserted-by":"crossref","first-page":"2956","DOI":"10.1529\/biophysj.106.087163","volume":"91","author":"S Kannan","year":"2006","unstructured":"Kannan S, Kohlhoff K, Zacharias M (2006) B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations. Biophys J 91(8):2956\u20132965. doi: 10.1529\/biophysj.106.087163","journal-title":"Biophys J"},{"issue":"4","key":"9828_CR41","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1006\/jmbi.1995.0388","volume":"250","author":"DB Starr","year":"1995","unstructured":"Starr DB, Hoopes BC, Hawley DK (1995) DNA bending ss an important component of site-specific recognition by the TATA-binding protein. J Mol Biol 250(4):434\u2013446. doi: 10.1006\/jmbi.1995.0388","journal-title":"J Mol Biol"},{"issue":"4","key":"9828_CR42","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1006\/jmbi.2001.4617","volume":"308","author":"XL Qian","year":"2001","unstructured":"Qian XL, Strahs D, Schlick T (2001) Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence\/activity relationships. J Mol Biol 308(4):681\u2013703. doi: 10.1006\/jmbi.2001.4617","journal-title":"J Mol Biol"},{"key":"9828_CR43","author":"SP Hancock","year":"2013","unstructured":"Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC (2013) Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucleic Acids Res. doi: 10.1093\/nar\/gkt357","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"9828_CR44","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1080\/07391102.2010.10507328","volume":"27","author":"S Samanta","year":"2010","unstructured":"Samanta S, Chakrabarti J, Bhattacharyya D (2010) Changes in thermodynamic properties of DNA base pairs in protein\u2013DNA recognition. J Biomol Struct Dyn 27(4):429\u2013442. doi: 10.1080\/07391102.2010.10507328","journal-title":"J Biomol Struct Dyn"},{"issue":"1","key":"9828_CR45","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235\u2013242. doi: 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"9828_CR46","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1080\/07391102.1996.10508916","volume":"13","author":"R Chandrasekaran","year":"1996","unstructured":"Chandrasekaran R, Arnott S (1996) The structure of B-DNA in oriented fibers. J Biomol Struct Dyn 13(6):1015\u20131027. doi: 10.1080\/07391102.1996.10508916","journal-title":"J Biomol Struct Dyn"},{"key":"9828_CR47","unstructured":"Case DA, VB JTB, Betz RM, Cai Q, Cerutti DS, Cheatham III TE, Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J, Kolossvary I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz Jr KM, Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL, Smith WL, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Kollman PA (2014) The FF14SB force field. AMBER 14 Reference Manual, pp 29\u201331"},{"issue":"1","key":"9828_CR48","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1006\/jcph.1999.6201","volume":"151","author":"L Kale","year":"1999","unstructured":"Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 151(1):283\u2013312. doi: 10.1006\/jcph.1999.6201","journal-title":"J Comput Phys"},{"issue":"1\u20133","key":"9828_CR49","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/0010-4655(95)00045-H","volume":"91","author":"M Nelson","year":"1995","unstructured":"Nelson M, Humphrey W, Kufrin R, Gursoy A, Dalke A, Kale L, Skeel R, Schulten K (1995) MDSCOPE\u2014a visual computing environment for structural biology. Comput Phys Commun 91(1\u20133):111\u2013133. doi: 10.1016\/0010-4655(95)00045-h","journal-title":"Comput Phys Commun"},{"issue":"19","key":"9828_CR50","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"117","author":"WD Cornell","year":"1995","unstructured":"Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179\u20135197. doi: 10.1021\/ja00124a002","journal-title":"J Am Chem Soc"},{"issue":"11","key":"9828_CR51","doi-asserted-by":"crossref","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","volume":"92","author":"A Perez","year":"2007","unstructured":"Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha\/gamma conformers. Biophys J 92(11):3817\u20133829. doi: 10.1529\/biophysj.106.097782","journal-title":"Biophys J"},{"issue":"2","key":"9828_CR52","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G","volume":"21","author":"N Foloppe","year":"2000","unstructured":"Foloppe N, MacKerell AD (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21(2):86\u2013104. doi: 10.1002\/(SICI)1096-987X(20000130)21:2<86:AID-JCC2>3.0.CO;2-G","journal-title":"J Comput Chem"},{"issue":"3","key":"9828_CR53","first-page":"281","volume":"11","author":"M Bansal","year":"1995","unstructured":"Bansal M, Bhattacharyya D, Ravi B (1995) NUPARM and NUCGEN\u2014software for analysis and generation of sequence-dependent nucleic-acid structures. Comput Appl Biosci 11(3):281\u2013287","journal-title":"Comput Appl Biosci"},{"issue":"10\u201311","key":"9828_CR54","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s10822-006-9083-x","volume":"20","author":"S Mukherjee","year":"2006","unstructured":"Mukherjee S, Bansal M, Bhattacharyya D (2006) Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Comput Aided Mol Des 20(10\u201311):629\u2013645. doi: 10.1007\/s10822-006-9083-x","journal-title":"J Comput Aided Mol Des"},{"issue":"20","key":"9828_CR55","doi-asserted-by":"crossref","first-page":"10484","DOI":"10.1021\/jp0446231","volume":"109","author":"S Mukherjee","year":"2005","unstructured":"Mukherjee S, Majumdar S, Bhattacharyya D (2005) Role of hydrogen bonds in protein\u2013DNA recognition: effect of nonplanar amino groups. J Phys Chem B 109(20):10484\u201310492. doi: 10.1021\/Jp0446231","journal-title":"J Phys Chem B"},{"issue":"12","key":"9828_CR56","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C (1983) Dictionary of protein secondary structure\u2014pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577\u20132637. doi: 10.1002\/bip.360221211","journal-title":"Biopolymers"},{"issue":"4","key":"9828_CR57","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1080\/07391102.1989.10507727","volume":"6","author":"D Bhattacharyya","year":"1989","unstructured":"Bhattacharyya D, Bansal M (1989) A self-consistent formulation for analysis and generation of non-uniform DNA structures. J Biomol Struct Dyn 6(4):635\u2013653. doi: 10.1080\/07391102.1989.10507727","journal-title":"J Biomol Struct Dyn"},{"issue":"10","key":"9828_CR58","doi-asserted-by":"crossref","first-page":"2647","DOI":"10.1093\/nar\/gkg362","volume":"31","author":"A Kanhere","year":"2003","unstructured":"Kanhere A, Bansal M (2003) An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data. Nucleic Acids Res 31(10):2647\u20132658. doi: 10.1093\/nar\/gkg362","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"9828_CR59","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1093\/nar\/26.8.1906","volume":"26","author":"RE Dickerson","year":"1998","unstructured":"Dickerson RE (1998) DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res 26(8):1906\u20131926. doi: 10.1093\/nar\/26.8.1906","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"9828_CR60","doi-asserted-by":"crossref","first-page":"5917","DOI":"10.1093\/nar\/gkp608","volume":"37","author":"R Lavery","year":"2009","unstructured":"Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K (2009) Conformational analysis of nucleic acids revisited: curves+. Nucleic Acids Res 37(17):5917\u20135929. doi: 10.1093\/nar\/gkp608","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"9828_CR61","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1002\/prot.22875","volume":"79","author":"L Skjaerven","year":"2011","unstructured":"Skjaerven L, Martinez A, Reuter N (2011) Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins Struct Funct Bioinf 79(1):232\u2013243. doi: 10.1002\/prot.22875","journal-title":"Proteins Struct Funct Bioinf"},{"issue":"21","key":"9828_CR62","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","volume":"22","author":"BJ Grant","year":"2006","unstructured":"Grant BJ, Rodrigues APC, ElSawy KM, McCammon JA, Caves LSD (2006) Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22(21):2695\u20132696. doi: 10.1093\/bioinformatics\/btl461","journal-title":"Bioinformatics"},{"issue":"11","key":"9828_CR63","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1002\/(SICI)1096-987X(199808)19:11<1255::AID-JCC5>3.0.CO;2-J","volume":"19","author":"OM Becker","year":"1998","unstructured":"Becker OM (1998) Principal coordinate maps of molecular potential energy surfaces. J Comput Chem 19(11):1255\u20131267. doi: 10.1002\/(sici)1096-987x(199808)19:11<1255:aid-jcc5>3.3.co;2-h","journal-title":"J Comput Chem"},{"key":"9828_CR64","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/biomet\/53.3-4.325","volume":"53","author":"JC Gower","year":"1966","unstructured":"Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325\u2013338. doi: 10.1093\/biomet\/53.3-4.325","journal-title":"Biometrika"},{"issue":"2","key":"9828_CR65","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1002\/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G","volume":"27","author":"OM Becker","year":"1997","unstructured":"Becker OM (1997) Geometric versus topological clustering: an insight into conformation mapping. Proteins Struct Funct Genet 27(2):213\u2013226. doi: 10.1002\/(sici)1097-0134(199702)27:2<213:aid-prot8>3.0.co;2-g","journal-title":"Proteins Struct Funct Genet"},{"issue":"8","key":"9828_CR66","doi-asserted-by":"crossref","first-page":"4256","DOI":"10.1128\/MCB.10.8.4256","volume":"10","author":"CJ Brandl","year":"1990","unstructured":"Brandl CJ, Struhl K (1990) A nucleosome-positioning sequence is required for GCN4 to activate transcription in the absence of a TATA element. Mol Cell Biol 10(8):4256\u20134265. doi: 10.1128\/MCB.10.8.4256","journal-title":"Mol Cell Biol"},{"key":"9828_CR67","author":"R Anish","year":"2009","unstructured":"Anish R, Hossain MB, Jacobson RH, Takada S (2009) Characterization of transcription from TATA-less promoters: identification of a new core promoter element XCPE2 and analysis of factor requirements. PLoS One. doi: 10.1371\/Journal.Pone.0005103","journal-title":"PLoS One"},{"key":"9828_CR68","doi-asserted-by":"crossref","unstructured":"Mondal M, Mukherjee S, Bhattacharyya D (2014) Contribution of phenylalanine side chain intercalation to the TATA-box binding protein-DNA interaction: molecular dynamics and dispersion-corrected density functional theory stidies. J Mol Model 20(11):2499. doi: 10.1007\/s00894-014-2499-7","DOI":"10.1007\/s00894-014-2499-7"},{"key":"9828_CR69","unstructured":"Calladine CR, Drew HR, Luisi BF, Travers AA (2004) Understanding DNA, the molecule and how it works, 3rd edn. Elsevier, London"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-014-9828-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-014-9828-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-014-9828-x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,26]],"date-time":"2022-04-26T13:53:39Z","timestamp":1650981219000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-014-9828-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,10]]},"references-count":69,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2015,3]]}},"alternative-id":["9828"],"URL":"https:\/\/doi.org\/10.1007\/s10822-014-9828-x","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,10]]}}}