Published in Nucleic Acids Res on February 24, 2008
Stability and kinetics of G-quadruplex structures. Nucleic Acids Res (2008) 2.75
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res (2009) 2.20
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Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res (2010) 1.40
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Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res (2011) 1.12
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Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res (2012) 1.10
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In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Res (2009) 1.09
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput (2013) 1.04
Toward a consensus view of duplex RNA flexibility. Biophys J (2010) 1.03
Impact of methylation on the physical properties of DNA. Biophys J (2012) 1.02
Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res (2009) 1.02
Parmbsc1: a refined force field for DNA simulations. Nat Methods (2015) 1.01
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Bullied no more: when and how DNA shoves proteins around. Q Rev Biophys (2012) 0.92
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Evaluation of DNA Force Fields in Implicit Solvation. J Chem Theory Comput (2011) 0.91
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics (2011) 0.89
NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res (2013) 0.88
Direct measurement of the dielectric polarization properties of DNA. Proc Natl Acad Sci U S A (2014) 0.87
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Res (2014) 0.86
The role of methylation in the intrinsic dynamics of B- and Z-DNA. PLoS One (2012) 0.86
Sequence dependencies of DNA deformability and hydration in the minor groove. Biophys J (2009) 0.84
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res (2016) 0.83
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Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy. J Phys Chem B (2012) 0.81
Assessing the Current State of Amber Force Field Modifications for DNA. J Chem Theory Comput (2016) 0.80
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Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study. Nucleic Acids Res (2013) 0.78
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The intrinsic mechanics of B-DNA in solution characterized by NMR. Nucleic Acids Res (2016) 0.78
Nucleic-acid structural deformability deduced from anisotropic displacement parameters. Biopolymers (2010) 0.77
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Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation. Nucleic Acids Res (2015) 0.75
Regulation of the activity of the promoter of RNA-induced silencing, C3PO. Protein Sci (2017) 0.75
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PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res (2003) 1.41
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Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure (2007) 1.24
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Begin at the beginning: predicting genes with 5' UTRs. Genome Res (2005) 1.14
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Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. BMC Genomics (2006) 0.91
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A consensus view of protein dynamics. Proc Natl Acad Sci U S A (2007) 1.73
Functional and structural conservation of CBS domains from CLC chloride channels. J Physiol (2004) 1.67
Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Res (2004) 1.53
The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res (2004) 1.52
Binding site detection and druggability index from first principles. J Med Chem (2009) 1.49
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chemistry (2006) 1.46
Determining promoter location based on DNA structure first-principles calculations. Genome Biol (2007) 1.44
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics (2011) 1.44
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Molecular basis of substrate-induced permeation by an amino acid antiporter. Proc Natl Acad Sci U S A (2011) 1.37
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Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J Mol Biol (2010) 1.26
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Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc (2003) 1.14
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Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily. Structure (2010) 1.11
Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res (2012) 1.10
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G-quadruplexes can maintain their structure in the gas phase. J Am Chem Soc (2006) 1.09
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res (2005) 1.08
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Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. J Med Chem (2011) 1.00
Nature of minor-groove binders-DNA complexes in the gas phase. J Am Chem Soc (2005) 1.00
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Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism. J Am Chem Soc (2005) 0.99
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Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water. Nucleic Acids Res (2007) 0.94
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Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B (2008) 0.93
Monte Carlo simulation of chromatin stretching. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.93
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Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res (2010) 0.92
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. BMC Genomics (2006) 0.91
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad. J Am Chem Soc (2003) 0.91
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Toward accurate relative energy predictions of the bioactive conformation of drugs. J Comput Chem (2009) 0.91
Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds. J Med Chem (2011) 0.90
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