Published in Biophys J on August 01, 2004
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The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res (2004) 1.52
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Determining promoter location based on DNA structure first-principles calculations. Genome Biol (2007) 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
Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys J (2004) 1.35
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Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res (2007) 1.29
Structure, recognition properties, and flexibility of the DNA.RNA hybrid. J Am Chem Soc (2005) 1.26
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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X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. J Chem Theory Comput (2009) 1.24
Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water. J Am Chem Soc (2005) 1.24
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure (2007) 1.24
Strong solute-solute dispersive interactions in a protein-ligand complex. J Am Chem Soc (2005) 1.19
The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol (2007) 1.17
Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One (2012) 1.16
Elucidation of thioredoxin as a molecular target for antitumor quinols. Cancer Res (2005) 1.13
The structure and dynamics of DNA in the gas phase. J Am Chem Soc (2003) 1.13
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (2010) 1.12
FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics (2009) 1.12
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
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
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics (2012) 1.07
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. J Am Chem Soc (2003) 1.06
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N. Proteins (2006) 1.06
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease. J Med Chem (2005) 1.05
Antitumor benzothiazoles. Frontier molecular orbital analysis predicts bioactivation of 2-(4-aminophenyl)benzothiazoles to reactive intermediates by cytochrome P4501A1. Org Biomol Chem (2003) 1.05
Relative flexibility of DNA and RNA: a molecular dynamics study. J Mol Biol (2004) 1.05
Synthetic lethal targeting of DNA double-strand break repair deficient cells by human apurinic/apyrimidinic endonuclease inhibitors. Int J Cancer (2012) 1.04
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput (2013) 1.04
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Antitumor polycyclic acridines. 8.(1) Synthesis and telomerase-inhibitory activity of methylated pentacyclic acridinium salts. J Med Chem (2002) 1.01
Nature of minor-groove binders-DNA complexes in the gas phase. J Am Chem Soc (2005) 1.00
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism. J Am Chem Soc (2005) 0.99
Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study. Chemistry (2005) 0.99
Design, synthesis, and biophysical and biological evaluation of a series of pyrrolobenzodiazepine-poly(N-methylpyrrole) conjugates. J Med Chem (2006) 0.99
Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species. J Mol Biol (2004) 0.99
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives. J Am Chem Soc (2002) 0.99
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol (2012) 0.96
Comparison of molecular dynamics and superfamily spaces of protein domain deformation. BMC Struct Biol (2009) 0.96
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water. Nucleic Acids Res (2007) 0.94
DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinformatics (2008) 0.94
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B (2008) 0.93
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. J Biol Chem (2007) 0.93
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. J Chem Inf Model (2011) 0.92
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
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad. J Am Chem Soc (2003) 0.91
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. BMC Genomics (2006) 0.91
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins (2005) 0.91
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility. J Am Chem Soc (2008) 0.90
Electrostatic component of solvation: comparison of SCRF continuum models. J Comput Chem (2003) 0.90
Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes. J Am Chem Soc (2004) 0.89
Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids. Angew Chem Int Ed Engl (2013) 0.89
Ligand-induced changes in the binding sites of proteins. Bioinformatics (2002) 0.89
Antitumor polycyclic acridines. 20. Search for DNA quadruplex binding selectivity in a series of 8,13-dimethylquino[4,3,2-kl]acridinium salts: telomere-targeted agents. J Med Chem (2008) 0.89
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics (2011) 0.89
Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. PLoS Comput Biol (2013) 0.88
NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res (2013) 0.88
Induction effects in metal cation-benzene complexes. Phys Chem Chem Phys (2008) 0.88
Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site? J Med Chem (2003) 0.87
The impact of monovalent ion force field model in nucleic acids simulations. Phys Chem Chem Phys (2009) 0.87
COCO: a simple tool to enrich the representation of conformational variability in NMR structures. Proteins (2009) 0.87
Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces. J Am Chem Soc (2002) 0.87
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling". Acc Chem Res (2009) 0.87
Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment. J Org Chem (2002) 0.87
Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution. J Am Chem Soc (2009) 0.87
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. J Am Chem Soc (2011) 0.87
Molecular modelling methods for prediction of sequence-selectivity in DNA recognition. Methods (2007) 0.86
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys J (2008) 0.86
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Res (2013) 0.86
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives. J Am Chem Soc (2003) 0.86
Cytochrome P450 Cyp4x1 is a major P450 protein in mouse brain. FEBS J (2006) 0.86
An atomistic view to the gas phase proteome. Structure (2009) 0.85
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines. Nucleic Acids Res (2002) 0.85
8-Amino guanine accelerates tetramolecular G-quadruplex formation. Chem Commun (Camb) (2008) 0.85