{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,6]],"date-time":"2023-09-06T18:33:33Z","timestamp":1694025213485},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Source Code Biol Med"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s13029-015-0040-8","type":"journal-article","created":{"date-parts":[[2015,9,25]],"date-time":"2015-09-25T03:49:33Z","timestamp":1443152973000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence"],"prefix":"10.1186","volume":"10","author":[{"given":"Connor H.","family":"Fortin","sequence":"first","affiliation":[]},{"given":"Katharina V.","family":"Schulze","sequence":"additional","affiliation":[]},{"given":"Gregory A.","family":"Babbitt","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,9,25]]},"reference":[{"key":"40_CR1","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/171740a0","volume":"171","author":"RE Franklin","year":"1953","unstructured":"Franklin RE, Gosling RG. Molecular configuration in sodium thymonucleate. Nature. 1953;171:740\u20131.","journal-title":"Nature"},{"key":"40_CR2","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/171737a0","volume":"171","author":"JD Watson","year":"1953","unstructured":"Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171:737\u20138.","journal-title":"Nature"},{"key":"40_CR3","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/171738a0","volume":"171","author":"MHF Wilkins","year":"1953","unstructured":"Wilkins MHF, Stokes AR, Wilson HR. Molecular structure of deoxypentose nucleic acids. Nature. 1953;171:738\u201340.","journal-title":"Nature"},{"key":"40_CR4","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","volume":"27","author":"CE Shannon","year":"1948","unstructured":"Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27:379\u2013423.","journal-title":"Bell Syst Tech J"},{"key":"40_CR5","doi-asserted-by":"crossref","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","volume":"18","author":"TD Schneider","year":"1990","unstructured":"Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990;18:6097\u2013100.","journal-title":"Nucleic Acids Res"},{"issue":"Web Server issu","key":"40_CR6","doi-asserted-by":"crossref","first-page":"W124","DOI":"10.1093\/nar\/gkl104","volume":"34","author":"S Ahmad","year":"2006","unstructured":"Ahmad S, Kono H, Ara\u00fazo-Bravo MJ, Sarai A. ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein\u2013DNA recognition. Nucleic Acids Res. 2006;34(Web Server issue):W124\u20137.","journal-title":"Nucleic Acids Res"},{"key":"40_CR7","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.jmb.2012.10.008","volume":"425","author":"L-A Harris","year":"2013","unstructured":"Harris L-A, Watkins D, Williams LD, Koudelka GB. Indirect readout of DNA sequence by p22 repressor: roles of DNA and protein functional groups in modulating DNA conformation. J Mol Biol. 2013;425:133\u201343.","journal-title":"J Mol Biol"},{"key":"40_CR8","doi-asserted-by":"crossref","first-page":"12955","DOI":"10.1074\/jbc.M212667200","volume":"278","author":"SA Mauro","year":"2003","unstructured":"Mauro SA, Pawlowski D, Koudelka GB. The Role of the Minor Groove Substituents in Indirect Readout of DNA Sequence by 434 Repressor. J Biol Chem. 2003;278:12955\u201360.","journal-title":"J Biol Chem"},{"issue":"suppl 1","key":"40_CR9","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1093\/bioinformatics\/18.suppl_1.S22","volume":"18","author":"NR Steffen","year":"2002","unstructured":"Steffen NR, Murphy SD, Tolleri L, Hatfield GW, Lathrop RH. DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics. 2002;18 suppl 1:S22\u201330.","journal-title":"Bioinformatics"},{"key":"40_CR10","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1021\/ci5000246","volume":"54","author":"H Yu","year":"2014","unstructured":"Yu H, Zhou P, Deng M, Shang Z. Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition. J Chem Inf Model. 2014;54:2022\u201332.","journal-title":"J Chem Inf Model"},{"key":"40_CR11","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/6707","volume":"6","author":"AM Martin","year":"1999","unstructured":"Martin AM, Sam MD, Reich NO, Perona JJ. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nat Struct Mol Biol. 1999;6:269\u201377.","journal-title":"Nat Struct Mol Biol"},{"key":"40_CR12","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1006\/jmbi.1998.1638","volume":"277","author":"A Bareket-Samish","year":"1998","unstructured":"Bareket-Samish A, Cohen I, Haran TE. Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites1. J Mol Biol. 1998;277:1071\u201380.","journal-title":"J Mol Biol"},{"key":"40_CR13","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1146\/annurev-biochem-060408-091030","volume":"79","author":"R Rohs","year":"2010","unstructured":"Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 2010;79:233\u201369.","journal-title":"Annu Rev Biochem"},{"key":"40_CR14","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/nature08473","volume":"461","author":"R Rohs","year":"2009","unstructured":"Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461:1248\u201353.","journal-title":"Nature"},{"key":"40_CR15","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1093\/nar\/gkp962","volume":"38","author":"B Heddi","year":"2010","unstructured":"Heddi B, Oguey C, Lavelle C, Foloppe N, Hartmann B. Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res. 2010;38:1034\u201347.","journal-title":"Nucleic Acids Res"},{"key":"40_CR16","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1093\/gbe\/evs073","volume":"4","author":"GA Babbitt","year":"2012","unstructured":"Babbitt GA, Schulze KV. Codons Support the Maintenance of Intrinsic DNA Polymer Flexibility over Evolutionary Timescales. Genome Biol Evol. 2012;4:954\u201365.","journal-title":"Genome Biol Evol"},{"key":"40_CR17","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.sbi.2014.01.007","volume":"25C","author":"M Bansal","year":"2014","unstructured":"Bansal M, Kumar A, Yella VR. Role of DNA sequence based structural features of promoters in transcription initiation and gene expression. Curr Opin Struct Biol. 2014;25C:77\u201385.","journal-title":"Curr Opin Struct Biol"},{"key":"40_CR18","doi-asserted-by":"crossref","unstructured":"Menconi G, Bedini A, Barale R, Sbrana I. Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae. PLoS Comput Biol. 2015;11.","DOI":"10.1371\/journal.pcbi.1004136"},{"key":"40_CR19","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.tig.2007.03.015","volume":"23","author":"I Tirosh","year":"2007","unstructured":"Tirosh I, Berman J, Barkai N. The pattern and evolution of yeast promoter bendability. Trends Genet TIG. 2007;23:318\u201321.","journal-title":"Trends Genet TIG"},{"key":"40_CR20","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1093\/nar\/gku811","volume":"42","author":"GA Babbitt","year":"2014","unstructured":"Babbitt GA, Alawad MA, Schulze KV, Hudson AO. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res. 2014;42:10915\u201326.","journal-title":"Nucleic Acids Res"},{"key":"40_CR21","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1080\/073911010010524947","volume":"27","author":"F Cui","year":"2010","unstructured":"Cui F, Zhurkin VB. Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro. J Biomol Struct Dyn. 2010;27:821\u201341.","journal-title":"J Biomol Struct Dyn"},{"key":"40_CR22","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/j.jmb.2007.05.048","volume":"371","author":"MY Tolstorukov","year":"2007","unstructured":"Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol. 2007;371:725\u201338.","journal-title":"J Mol Biol"},{"key":"40_CR23","doi-asserted-by":"crossref","first-page":"11163","DOI":"10.1073\/pnas.95.19.11163","volume":"95","author":"WK Olson","year":"1998","unstructured":"Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A. 1998;95:11163\u20138.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"40_CR24","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/S0006-3495(97)78049-4","volume":"73","author":"J Sponer","year":"1997","unstructured":"Sponer J, Gabb HA, Leszczynski J, Hobza P. Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys J. 1997;73:76\u201387.","journal-title":"Biophys J"},{"key":"40_CR25","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1126\/science.1169050","volume":"324","author":"SCJ Parker","year":"2009","unstructured":"Parker SCJ, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome. Science. 2009;324:389\u201392.","journal-title":"Science"},{"key":"40_CR26","doi-asserted-by":"crossref","first-page":"9273","DOI":"10.1073\/pnas.86.23.9273","volume":"86","author":"ME Hogan","year":"1989","unstructured":"Hogan ME, Roberson MW, Austin RH. DNA flexibility variation may dominate DNase I cleavage. Proc Natl Acad Sci U S A. 1989;86:9273\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"40_CR27","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.gene.2010.07.002","volume":"466","author":"GA Babbitt","year":"2010","unstructured":"Babbitt GA. Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene. 2010;466:43\u20138.","journal-title":"Gene"},{"key":"40_CR28","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/gbe\/evq081","volume":"3","author":"GA Babbitt","year":"2011","unstructured":"Babbitt GA, Cotter CR. Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes. Genome Biol Evol. 2011;3:15\u201322.","journal-title":"Genome Biol Evol"},{"key":"40_CR29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004457","volume":"10","author":"SA Langley","year":"2014","unstructured":"Langley SA, Karpen GH, Langley CH. Nucleosomes Shape DNA Polymorphism and Divergence. PloS Genet. 2014;10:e1004457.","journal-title":"PloS Genet"},{"key":"40_CR30","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1093\/nar\/gkg296","volume":"31","author":"AE Vinogradov","year":"2003","unstructured":"Vinogradov AE. DNA helix: the importance of being GC\u2010rich. Nucleic Acids Res. 2003;31:1838\u201344.","journal-title":"Nucleic Acids Res"},{"key":"40_CR31","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/bioinformatics\/btt463","volume":"29","author":"RA Salama","year":"2013","unstructured":"Salama RA, Stekel DJ. A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites. Bioinformatics. 2013;29:2699\u2013704.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"40_CR32","doi-asserted-by":"crossref","first-page":"D148","DOI":"10.1093\/nar\/gkt1087","volume":"42","author":"L Yang","year":"2014","unstructured":"Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gord\u00e2n R, et al. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014;42(Database issue):D148\u2013155.","journal-title":"Nucleic Acids Res"},{"key":"40_CR33","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.nancom.2010.09.002","volume":"1","author":"TD Schneider","year":"2010","unstructured":"Schneider TD. A brief review of molecular information theory. Nano Commun Netw. 2010;1:173\u201380.","journal-title":"Nano Commun Netw"},{"key":"40_CR34","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s12038-012-9222-6","volume":"37","author":"DL Beveridge","year":"2012","unstructured":"Beveridge DL, Cheatham TE, Mezei M. The ABCs of molecular dynamics simulations on B-DNA, circa 2012. J Biosci. 2012;37:379\u201397.","journal-title":"J Biosci"},{"key":"40_CR35","doi-asserted-by":"crossref","first-page":"12272","DOI":"10.1093\/nar\/gku855","volume":"42","author":"M Pasi","year":"2014","unstructured":"Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, et al. \u03bcABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res. 2014;42:12272\u201383.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"40_CR36","doi-asserted-by":"crossref","first-page":"D91","DOI":"10.1093\/nar\/gkh012","volume":"32","author":"A Sandelin","year":"2004","unstructured":"Sandelin A, Alkema W, Engstr\u00f6m P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004;32(Database issue):D91\u201394.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"40_CR37","doi-asserted-by":"crossref","first-page":"D446","DOI":"10.1093\/nar\/gkj013","volume":"34","author":"MC Teixeira","year":"2006","unstructured":"Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006;34 suppl 1:D446\u201351.","journal-title":"Nucleic Acids Res"},{"key":"40_CR38","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","volume":"30","author":"K Tamura","year":"2013","unstructured":"Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013;30:2725\u20139.","journal-title":"Mol Biol Evol"},{"key":"40_CR39","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature01644","volume":"423","author":"M Kellis","year":"2003","unstructured":"Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003;423:241\u201354.","journal-title":"Nature"},{"key":"40_CR40","doi-asserted-by":"crossref","first-page":"2866","DOI":"10.1128\/MCB.12.6.2866","volume":"12","author":"WD Funk","year":"1992","unstructured":"Funk WD, Pak DT, Karas RH, Wright WE, Shay JW. A transcriptionally active DNA-binding site for human p53 protein complexes. Mol Cell Biol. 1992;12:2866\u201371.","journal-title":"Mol Cell Biol"},{"key":"40_CR41","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1745-6150-6-2","volume":"6","author":"F Cui","year":"2011","unstructured":"Cui F, Sirotin MV, Zhurkin VB. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct. 2011;6:2.","journal-title":"Biol Direct"},{"key":"40_CR42","doi-asserted-by":"crossref","unstructured":"Schlereth K, Heyl C, Krampitz A-M, Mernberger M, Finkernagel F, Scharfe M, et al. Characterization of the p53 Cistrome \u2013 DNA Binding Cooperativity Dissects p53\u2032s Tumor Suppressor Functions. PLoS Genet. 2013;9.","DOI":"10.1371\/journal.pgen.1003726"}],"container-title":["Source Code for Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13029-015-0040-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T23:37:13Z","timestamp":1567208233000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.scfbm.org\/content\/10\/1\/10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,9,25]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["40"],"URL":"https:\/\/doi.org\/10.1186\/s13029-015-0040-8","relation":{},"ISSN":["1751-0473"],"issn-type":[{"value":"1751-0473","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,25]]},"article-number":"10"}}