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Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput (2012) 1.93

Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res (2008) 1.56

Structural equilibrium of DNA represented with different force fields. Biophys J (1998) 1.49

Alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res (2002) 1.36

Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element. Nucleic Acids Res (2001) 1.21

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res (2014) 1.16

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput (2013) 1.09

Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res (2009) 1.02

Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B (2009) 1.01

Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC). Nucleic Acids Res (2005) 1.01

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochim Biophys Acta (2014) 0.98

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. Nucleic Acids Res (2011) 0.97

31P NMR investigation of backbone dynamics in DNA binding sites. J Phys Chem B (2009) 0.97

The phosphate clamp: a small and independent motif for nucleic acid backbone recognition. Nucleic Acids Res (2010) 0.96

Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove. J Biomol Struct Dyn (2010) 0.93

Evaluation of DNA Force Fields in Implicit Solvation. J Chem Theory Comput (2011) 0.91

Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One (2010) 0.91

The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex. Nucleic Acids Res (2002) 0.88

Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism. Biophys J (2005) 0.88

Theoretical studies of DNA-RNA hybrid conformations. Nucleic Acids Res (1994) 0.86

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Res (2013) 0.86

The role of methylation in the intrinsic dynamics of B- and Z-DNA. PLoS One (2012) 0.86

Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J Phys Chem B (2012) 0.86

New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex. Nucleic Acids Res (2005) 0.84

Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics. Nucleic Acids Res (1997) 0.84

Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One (2012) 0.82

DNA structures from phosphate chemical shifts. Nucleic Acids Res (2009) 0.81

Calculated distortions of duplex DNA by a cis, syn cyclobutane thymine dimer are unaffected by a 3' TpA step. Nucleic Acids Res (1997) 0.81

Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR. Biophys J (2000) 0.81

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding. J Chem Theory Comput (2015) 0.80

Structure of d(CGGGTACCCG)4 as a four-way Holliday junction. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.80

An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites. Biochemistry (2009) 0.78

Phosphorus-31 transverse relaxation rate measurements by NMR spectroscopy: insight into conformational exchange along the nucleic acid backbone. J Biomol NMR (2004) 0.78

The intrinsic mechanics of B-DNA in solution characterized by NMR. Nucleic Acids Res (2016) 0.78

On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics. Nucleic Acids Res (2010) 0.76

Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA. Nucleic Acids Res (2014) 0.75

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics. PLoS Comput Biol (2015) 0.75

Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations. J Mol Model (2017) 0.75

The "sugar" coarse-grained DNA model. J Mol Model (2017) 0.75

Identification of a cyclic-AMP-responsive element within the rat somatostatin gene. Proc Natl Acad Sci U S A (1986) 10.41

Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn (1989) 5.52

The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. J Biol Chem (1991) 2.89

Energetic coupling between DNA bending and base pair opening. Proc Natl Acad Sci U S A (1988) 2.84

Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science (1987) 2.77

Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J Mol Biol (1991) 2.34

Transcription factors: a new family gathers at the cAMP response site. Trends Genet (1990) 2.28

Crystallographic study of one turn of G/C-rich B-DNA. J Mol Biol (1989) 1.69

The effect of crystal packing on oligonucleotide double helix structure. J Biomol Struct Dyn (1987) 1.64

Conformational flexibility of DNA: polymorphism and handedness. Proc Natl Acad Sci U S A (1980) 1.55

The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA. J Biomol Struct Dyn (1986) 1.50

C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G. J Biol Chem (1992) 1.39

Determination of nucleic acid backbone conformation by 1H NMR. Biochemistry (1992) 1.38

A general approach to the optimization of the conformation of ring molecules with an application to valinomycin. J Biomol Struct Dyn (1986) 1.23

Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on 31P NMR spectra. Biochemistry (1990) 1.22

Definitions and nomenclature of nucleic acid structure parameters. J Mol Biol (1989) 1.22

Effect of crystal packing environment on conformation of the DNA duplex. Molecular structure of the A-DNA octamer d(G-T-G-T-A-C-A-C) in two crystal forms. J Biol Chem (1989) 1.19

Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex. Biochemistry (1990) 1.06

Investigations on the dynamic structures of adenine- and thymine-containing DNA. J Mol Biol (1992) 0.91

Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies. J Mol Biol (1989) 0.90

Static and dynamic conformational properties of AT sequences in B-DNA. J Biomol Struct Dyn (1992) 0.88

Triple helix structures: sequence dependence, flexibility and mismatch effects. J Biomol Struct Dyn (1991) 0.85

DNA: an extensible molecule. Science (1996) 8.19

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows. J Biomol Struct Dyn (1989) 3.78

Energetic coupling between DNA bending and base pair opening. Proc Natl Acad Sci U S A (1988) 2.84

A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dyn (1991) 2.79

Modelling extreme stretching of DNA. Nucleic Acids Res (1996) 2.69

Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc Natl Acad Sci U S A (1998) 2.35

Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071. Nucleic Acids Res (1983) 1.73

Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins (1989) 1.70

Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc Natl Acad Sci U S A (1997) 1.47

Unraveling proteins: a molecular mechanics study. Biophys J (1999) 1.43

Measuring the geometry of DNA grooves. Biopolymers (1994) 1.40

Generalised reduction of putative endothelial progenitors and CXCR4-positive peripheral blood cells in type 2 diabetes. Diabetologia (2008) 1.22

Conformational sub-states in B-DNA. J Mol Biol (1992) 1.15

Prospective randomized trial of thoracostomy removal algorithms. J Trauma (1999) 1.14

The electrostatic potential and steric accessibility of reactive sites within Z-DNA. Nucleic Acids Res (1980) 1.11

Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature. Nucleic Acids Res (1996) 1.10

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix. Chemphyschem (2001) 1.10

Non-additivity in protein-DNA binding. Bioinformatics (2005) 1.09

DNA structural forms. Q Rev Biophys (1996) 1.08

Magnesium sulfate in the treatment of refractory ventricular fibrillation in the prehospital setting. Resuscitation (2001) 1.04

A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix. Biochemistry (1993) 1.02

From atomic to mesoscopic descriptions of the internal dynamics of DNA. Biophys J (1999) 1.01

A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys J (1999) 1.01

Two aspects of DNA polymorphism and microheterogeneity: molecular electrostatic potential and steric accessibility. Eur J Biochem (1982) 1.01

The electrostatic molecular potential of yeast tRNAPhe. (I). The potential due to the phosphate backbone. Nucleic Acids Res (1980) 1.00

The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases. Nucleic Acids Res (1980) 1.00

Ureteral trauma: preoperative studies neither predict injury nor prevent missed injuries. J Am Coll Surg (1998) 0.97

The flexibility of the nucleic acids: (I). "SIR", a novel approach to the variation of polymer geometry in constrained systems. J Biomol Struct Dyn (1986) 0.96

Genetics of ovarian differentiation: Rspo1, a major player. Sex Dev (2008) 0.96

A new theoretical index of biochemical reactivity combining steric and electrostatic factors. An application to yeast tRNAPhe. Biophys Chem (1984) 0.95

The molecular electrostatic potential and steric accessibility of A-DNA. Nucleic Acids Res (1981) 0.95

A computational and experimental study of the bending induced at a double-triple helix junction. Biophys Chem (1992) 0.93

Sequence-dependent dynamics of TATA-Box binding sites. Biophys J (1998) 0.93

Optimization of nucleic acid sequences. Biophys J (2000) 0.93

ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences. Biopolymers (2001) 0.93

Conformational properties of the TATA-box binding sequence of DNA. J Biomol Struct Dyn (1997) 0.91

The impact of abasic sites on DNA flexibility. J Biomol Struct Dyn (2000) 0.91

Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline conjugates: parallel and antiparallel double helices are formed with DNA and RNA, respectively. Biochemistry (1988) 0.91

Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies. J Mol Biol (1989) 0.90

The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG). Nucleic Acids Res (1981) 0.89

Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides. Biophys Chem (1982) 0.89

DNA stem-loop structures in oligopurine-oligopyrimidine triplexes. Nucleic Acids Res (1988) 0.89

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation. Biophys J (1999) 0.89

Unusual DNA conformations. Curr Opin Struct Biol (1997) 0.88

Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA. Protein Eng (2001) 0.87

Base pair opening pathways in B-DNA. J Biomol Struct Dyn (1990) 0.87

The molecular electrostatic potential and steric accessibility of poly (dA-dT). poly (dA-dT) in various conformations: B-DNA, D-DNA and 'alternating-B' DNA. Nucleic Acids Res (1981) 0.87

Modeling the mechanics of a DNA oligomer. J Biomol Struct Dyn (1998) 0.87

Theoretical studies of DNA-RNA hybrid conformations. Nucleic Acids Res (1994) 0.86

A preliminary report on the implication of RT-PCR detection of DAZ, RBMY1, USP9Y and Protamine-2 mRNA in testicular biopsy samples from azoospermic men. Int J Androl (2002) 0.86

The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse. Nuclear magnetic resonance and molecular simulation studies. J Mol Biol (1992) 0.85

DNA flexibility as a function of allomorphic conformation and of base sequence. Biopolymers (1992) 0.85

Triple helix structures: sequence dependence, flexibility and mismatch effects. J Biomol Struct Dyn (1991) 0.85

Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers (1993) 0.85

The effects of countercation screening on the electrostatic potential of DNA. The rôle of the nucleic acid conformation. FEBS Lett (1982) 0.84

Collective variable modelling of nucleic acids. Curr Opin Struct Biol (1999) 0.84

The electrostatic field of the component units of DNA and its relationship to hydration. Biophys Chem (1983) 0.84

Modeling DNA deformations induced by minor groove binding proteins. Biopolymers (1999) 0.84

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study. J Mol Biol (1994) 0.83

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI. Proteins (1990) 0.83

Role of interleukin 8 in the genesis of acute respiratory distress syndrome through an effect on neutrophil apoptosis. Arch Surg (1998) 0.82

A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J Biomol Struct Dyn (1998) 0.82

High-speed molecular mechanics searches for optimal DNA interaction sites. Comb Chem High Throughput Screen (2001) 0.81

The solvation contribution to the binding energy of DNA with non-intercalating antibiotics. Nucleic Acids Res (1984) 0.80

The molecular electrostatic potential and steric accessibility of poly (dI.dC). Comparison with poly (dG.dC). Nucleic Acids Res (1981) 0.80

Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions. J Biomol Struct Dyn (1991) 0.80

Guanine and 7-methylguanine amino proton exchange rates as a function of buffer pK: implications for the exchange mechanism. Nucleic Acids Res (1986) 0.80

The molecular electrostatic potential and steric accessibility of double-helical A-RNA. Biochim Biophys Acta (1982) 0.79

Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin. Proteins (1993) 0.79

The electrostatic field of DNA: the role of the nucleic acid conformation. Nucleic Acids Res (1982) 0.79

A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via Triple-Helical Intermediates. J Biomol Struct Dyn (2000) 0.79

Storage temperatures of medications on an air medical helicopter. Air Med J (2000) 0.79

ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes. Proteins (2006) 0.79

Strand orientation of [alpha]-oligodeoxynucleotides in triple helix structures: dependence on nucleotide sequence. J Mol Recognit (1992) 0.78

Experimental and theoretical studies of the conformational perturbations induced by an abasic site. J Biomol Struct Dyn (1999) 0.78

Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: an internal coordinate molecular modeling study. J Biomol Struct Dyn (1997) 0.78

Role of granulocyte-macrophage colony-stimulating factor and its receptor in the genesis of acute respiratory distress syndrome through an effect on neutrophil apoptosis. Arch Surg (1999) 0.78

Storage temperatures of out-of-hospital medications. Acad Emerg Med (1999) 0.77

A theoretical study of the sequence specificity in binding of lexitropsins to B-DNA. J Biomol Struct Dyn (1987) 0.77

An analysis of the conformational paths of citrate synthase. Proteins (1993) 0.77

Modeling a strand exchange tetraplex conformation. J Biomol Struct Dyn (1995) 0.76

What is the patient's charter? Med Leg J (1992) 0.75

Postsplenectomy sepsis: a case review and one hospital's campaign to prevent other needless tragedies. J Emerg Nurs (1991) 0.75

The conformation and stability of ribonucleic acids: modeling base sequence effects in double stranded helices. J Biomol Struct Dyn (1989) 0.75

Studies of the dependence of the internal energy of DNA on its conformation. Prog Clin Biol Res (1985) 0.75

Theoretical studies on the interaction of proteins and nucleic acid. II. The binding of alpha-helix to B-DNA. Biophys Chem (1986) 0.75

Conformations of DNA duplexes containing 8-oxoguanine. J Biomol Struct Dyn (1993) 0.75

Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories. Biopolymers (1995) 0.75