Published in PLoS One on July 23, 2012
A repulsion mechanism explains magnesium permeation and selectivity in CorA. Proc Natl Acad Sci U S A (2014) 0.84
All-atom crystal simulations of DNA and RNA duplexes. Biochim Biophys Acta (2014) 0.79
Force regulated dynamics of RPA on a DNA fork. Nucleic Acids Res (2016) 0.77
Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction. DNA Repair (Amst) (2016) 0.76
A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity. FEBS Open Bio (2016) 0.75
Atomic level rendering of DNA-drug encounter. Biophys J (2014) 0.75
Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One (2017) 0.75
Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A (2001) 42.14
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J (2007) 7.99
The structure of DNA in the nucleosome core. Nature (2003) 7.94
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn (1999) 5.14
Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res (2009) 3.76
Ions and RNA folding. Annu Rev Biophys Biomol Struct (2005) 3.37
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
Molecular electrostatic potential of the nucleic acids. Q Rev Biophys (1981) 2.29
DNA and its counterions: a molecular dynamics study. Nucleic Acids Res (2004) 2.27
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J Am Chem Soc (2007) 2.20
Ion motions in molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A (2004) 2.19
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. Biophys J (2005) 2.09
Water and ion binding around RNA and DNA (C,G) oligomers. J Mol Biol (2000) 1.86
Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J Mol Biol (1999) 1.67
1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J Mol Biol (2000) 1.63
Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. J Mol Biol (1999) 1.63
BI-BII transitions in B-DNA. Nucleic Acids Res (1993) 1.56
DNA-cation interactions: The major and minor grooves are flexible ionophores. Curr Opin Struct Biol (2001) 1.54
DNA-dependent divalent cation binding in the nucleosome core particle. Proc Natl Acad Sci U S A (2002) 1.39
Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex. J Mol Biol (1999) 1.37
Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J Mol Biol (1992) 1.36
Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G. J Mol Biol (1999) 1.35
BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA. J Mol Biol (2000) 1.34
Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). J Mol Biol (2000) 1.30
Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J Mol Biol (1994) 1.27
DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers (2004) 1.25
Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA. Biochemistry (1993) 1.24
Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. J Mol Biol (2001) 1.20
DNA-cation interactions: quo vadis? Chem Biol (2002) 1.20
Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition. J Am Chem Soc (2006) 1.18
Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states. J Biomol Struct Dyn (2003) 1.13
Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. J Mol Biol (1998) 1.11
Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. Annu Rev Biophys Biomol Struct (2003) 1.10
Importance of accurate DNA structures in solution: the Jun-Fos model. J Mol Biol (2008) 1.09
Metal ion binding to RNA. Met Ions Life Sci (2011) 1.03
Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res (2009) 1.02
Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA. Biophys Rev (2009) 1.01
Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution. J Biol Chem (2000) 1.00
Strained DNA is kinked by low concentrations of Zn2+. Proc Natl Acad Sci U S A (1997) 0.99
A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Res (2010) 0.99
Structure of d(CGCGAATTCGCG) in the presence of Ca(2+) ions. J Biol Chem (1999) 0.97
Sequence-selective metal ion binding to DNA oligonucleotides. Acta Chem Scand (1993) 0.95
The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol (2007) 0.93
A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings. Biophys J (2003) 0.93
Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One (2010) 0.91
Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions. Nucleic Acids Res (1999) 0.91
Differential stability of DNA crossovers in solution mediated by divalent cations. Nucleic Acids Res (2010) 0.89
Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion. J Biomol Struct Dyn (1999) 0.88
Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome. J Mol Biol (2010) 0.87
The interaction of manganese ions with DNA. J Inorg Biochem (2009) 0.87
Magnesium increases the curvature of duplex DNA that contains dA tracts. Biochemistry (2001) 0.85
Sequence-selective metal ion binding to DNA hexamers. Acta Chem Scand (1994) 0.83
DNA structures from phosphate chemical shifts. Nucleic Acids Res (2009) 0.81
The binding of manganese(II) and zinc(II) to the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2. A 1H NMR study. Acta Chem Scand (1991) 0.81
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides. Nucleic Acids Res (2006) 0.78
On the orientation of a designed transmembrane peptide: toward the right tilt angle? J Am Chem Soc (2007) 1.54
Determining membrane protein structures: still a challenge! Trends Biochem Sci (2007) 1.50
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J (2002) 1.40
Alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res (2002) 1.36
Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J (2013) 1.19
Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition. J Am Chem Soc (2006) 1.18
Conical lipids in flat bilayers induce packing defects similar to that induced by positive curvature. Biophys J (2013) 1.10
A short survey on protein blocks. Biophys Rev (2010) 1.10
Importance of accurate DNA structures in solution: the Jun-Fos model. J Mol Biol (2008) 1.09
Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res (2009) 1.02
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol (2008) 1.02
Sequence-dependent DNA flexibility mediates DNase I cleavage. J Mol Biol (2009) 0.99
Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. Protein Sci (2002) 0.99
Local backbone structure prediction of proteins. In Silico Biol (2004) 0.98
Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel. Structure (2010) 0.95
PredyFlexy: flexibility and local structure prediction from sequence. Nucleic Acids Res (2012) 0.94
The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol (2007) 0.93
Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One (2010) 0.91
Theoretical model of human apolipoprotein B100 tertiary structure. Proteins (2007) 0.91
Structural model of the anion exchanger 1 (SLC4A1) and identification of transmembrane segments forming the transport site. J Biol Chem (2013) 0.88
Assessing a novel approach for predicting local 3D protein structures from sequence. Proteins (2006) 0.88
Predicting protein flexibility through the prediction of local structures. Proteins (2010) 0.87
Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes. Proteins (2008) 0.86
An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression. J Gene Med (2009) 0.85
A new prediction strategy for long local protein structures using an original description. Proteins (2009) 0.85
New insights of membrane environment effects on MscL channel mechanics from theoretical approaches. Proteins (2008) 0.84
Amphipathic-Lipid-Packing-Sensor interactions with lipids assessed by atomistic molecular dynamics. Biochim Biophys Acta (2011) 0.84
Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin. Biophys J (2005) 0.82
Clustering of protein domains for functional and evolutionary studies. BMC Bioinformatics (2009) 0.81
Aminopeptidase B, a glucagon-processing enzyme: site directed mutagenesis of the Zn2+-binding motif and molecular modelling. BMC Biochem (2007) 0.81
DNA structures from phosphate chemical shifts. Nucleic Acids Res (2009) 0.81
NMR studies of DNA support the role of pre-existing minor groove variations in nucleosome indirect readout. Biochemistry (2014) 0.80
Simulating DNA by molecular dynamics: aims, methods, and validation. Methods Mol Biol (2013) 0.80
How cations can assist DNase I in DNA binding and hydrolysis. PLoS Comput Biol (2010) 0.79
Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac Symp Biocomput (2010) 0.79
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PLoS One (2011) 0.78
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides. Nucleic Acids Res (2006) 0.78
Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations. Proteins (2014) 0.78
Ets-1 p51 and p42 isoforms differentially modulate Stromelysin-1 promoter according to induced DNA bend orientation. Nucleic Acids Res (2009) 0.78
A procedure for refining a coiled coil protein structure using x-ray fiber diffraction and modeling. Biophys J (2002) 0.78
In silico studies on DARC. Infect Disord Drug Targets (2009) 0.78
Influence of assignment on the prediction of transmembrane helices in protein structures. Amino Acids (2010) 0.78
Discrimination between BI and BII conformational substates of B-DNA based on sugar-base interproton distances. J Biomol Struct Dyn (2004) 0.77
Mutation in the substrate-binding site of aminopeptidase B confers new enzymatic properties. Biochimie (2011) 0.75