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influence of the crystal environment","volume":"78","author":"DR Bevan","year":"2000","journal-title":"Biophys J"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref57","unstructured":"Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, <etal>et al<\/etal>.. 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I. Folding behavior in water solution","volume":"810","author":"H Rundgren","year":"2007","journal-title":"J Mol Struct: Theochem"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1002\/prot.21552","article-title":"Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain","volume":"70","author":"P Del Vecchio","year":"2008","journal-title":"Proteins"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/bip.10242","article-title":"Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA","volume":"68","author":"W Flader","year":"2003","journal-title":"Biopolymers"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s00249-012-0790-z","article-title":"Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations","volume":"41","author":"S Jalili","year":"2012","journal-title":"Eur Biophys J"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1016\/j.jmgm.2011.03.003","article-title":"Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA","volume":"29","author":"SY Yang","year":"2011","journal-title":"J Mol Graph Model"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.sbi.2004.05.001","article-title":"Simulation and modeling of nucleic acid structure, dynamics and interactions","volume":"14","author":"TE Cheatham","year":"2004","journal-title":"Curr Opin Struc Biol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1146\/annurev.physchem.51.1.435","article-title":"Molecular dynamics simulation of nucleic acids","volume":"51","author":"TE Cheatham","year":"2000","journal-title":"Annu Rev Phys Chem"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"3721","DOI":"10.1529\/biophysj.105.067397","article-title":"Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps","volume":"89","author":"SB Dixit","year":"2005","journal-title":"Biophys J"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"1609191","DOI":"10.1063\/1.1609191","article-title":"Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles","volume":"119","author":"DH Herce","year":"2003","journal-title":"J Chem Phys"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"214103","DOI":"10.1063\/1.3595262","article-title":"A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent","volume":"134","author":"JA Wagoner","year":"2011","journal-title":"J Chem Phys"},{"key":"ref87","doi-asserted-by":"crossref","unstructured":"Karttunen J, Rottler J, Vattulainen I, Sagui C (2008) Electrostatics in biomolecular simulations: Where are we now and where are we heading? In: Feller SE, editor. Current topics in membranes. Burlington: Academic Press. pp. 49\u201389.","DOI":"10.1016\/S1063-5823(08)00002-1"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1146\/annurev.biophys.28.1.155","article-title":"Molecular dynamics simulations of biomolecules: long-range electrostatic effects","volume":"28","author":"C Sagui","year":"1999","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/0009-2614(95)00845-U","article-title":"Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides -ApU and GpC","volume":"243","author":"H Lee","year":"1995","journal-title":"Chem Phys Let"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"3830","DOI":"10.1063\/1.468564","article-title":"Molecular dynamics simulation studies of a high resolution Z-DNA crystal","volume":"102","author":"H Lee","year":"1995","journal-title":"J Chem Phys"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"8715","DOI":"10.1073\/pnas.91.18.8715","article-title":"Atomic-level accuracy in simulations of large protein crystals","volume":"91","author":"DM York","year":"1994","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"5001","DOI":"10.1021\/ja00122a034","article-title":"Toward the accurate modeling of DNA: the importance of long-range electrostatics","volume":"117","author":"DM York","year":"1995","journal-title":"J Am Chem Soc"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1002\/prot.10375","article-title":"Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA","volume":"51","author":"J Aishima","year":"2003","journal-title":"Proteins"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"2060","DOI":"10.1101\/gad.1103303","article-title":"Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior","volume":"17","author":"NA LaRonde-LeBlanc","year":"2003","journal-title":"Genes Dev"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/S0092-8674(00)80662-5","article-title":"Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation","volume":"96","author":"DE Piper","year":"1999","journal-title":"Cell"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"4093","DOI":"10.1073\/pnas.87.11.4093","article-title":"DNA binding properties of the purified Antennapedia homeodomain","volume":"87","author":"M Affolter","year":"1990","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1101\/gad.9.2.182","article-title":"A homeo domain protein lacking specific side chains of helix 3 can still bind DNA and direct transcriptional repression","volume":"9","author":"AK Vershon","year":"1995","journal-title":"Genes Dev"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"22228","DOI":"10.1074\/jbc.M312673200","article-title":"Identification of a novel PDX-1 binding site in the human insulin gene enhancer","volume":"279","author":"J Le Lay","year":"2004","journal-title":"J Biol Chem"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"4992","DOI":"10.1002\/j.1460-2075.1996.tb00879.x","article-title":"A molecular code dictates sequence-specific DNA recognition by homeodomains","volume":"15","author":"G Damante","year":"1996","journal-title":"EMBO J"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1021\/bi051705m","article-title":"Forces driving the binding of homeodomains to DNA","volume":"45","author":"AI Dragan","year":"2006","journal-title":"Biochemistry"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"3551","DOI":"10.1002\/j.1460-2075.1994.tb06662.x","article-title":"The degree of variation in DNA 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