Published in Phys Chem Chem Phys on September 24, 2009
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B (2010) 1.11
Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B (2010) 1.10
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput (2012) 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
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res (2011) 1.02
Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods (2012) 0.98
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res (2010) 0.97
Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B (2010) 0.93
Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res (2012) 0.91
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. J Chem Theory Comput (2010) 0.90
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure. J Biomol NMR (2012) 0.84
Substrate recognition and specificity of double-stranded RNA binding proteins. Biochemistry (2014) 0.81
Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res (2014) 0.81
Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. PLoS Comput Biol (2011) 0.80
All-atom crystal simulations of DNA and RNA duplexes. Biochim Biophys Acta (2014) 0.79
Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations. Biophys J (2014) 0.77
Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex. J Am Chem Soc (2016) 0.76
Revised RNA dihedral parameters for the Amber force field improve RNA molecular dynamics. J Chem Theory Comput (2017) 0.75
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics (2006) 4.11
Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. Chem Rev (2012) 3.19
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys (2006) 2.55
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (2007) 2.49
DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J (2003) 2.12
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J (2006) 1.54
Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J Am Chem Soc (2002) 1.54
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys J (2003) 1.46
Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers (2007) 1.41
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res (2010) 1.40
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat Chem Biol (2009) 1.39
Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys J (2003) 1.38
Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc Natl Acad Sci U S A (2006) 1.34
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res (2012) 1.34
Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J (2004) 1.33
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnol J (2007) 1.31
Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res (2006) 1.30
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases. Biophys J (2005) 1.27
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform (2013) 1.26
Ribosomal RNA kink-turn motif--a flexible molecular hinge. J Biomol Struct Dyn (2004) 1.23
Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site. J Phys Chem A (2011) 1.21
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J Mol Biol (2005) 1.20
Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry (2004) 1.19
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure (2006) 1.17
Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences. J Phys Chem B (2008) 1.16
Environmental applications of chemically pure natural ferrihydrite. Environ Sci Technol (2007) 1.15
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
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res (2003) 1.14
Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? J Phys Chem B (2010) 1.12
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers (2006) 1.11
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B (2010) 1.11
Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J Phys Chem B (2005) 1.10
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput (2012) 1.09
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput (2013) 1.09
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. RNA (2009) 1.08
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
Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophys J (2002) 1.07
Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop. Protein Sci (2004) 1.04
Adsorption of small organic molecules on graphene. J Am Chem Soc (2013) 1.04
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr Drug Metab (2012) 1.02
Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys Chem Chem Phys (2010) 1.02
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res (2013) 1.02
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys J (2007) 1.00
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys J (2004) 1.00
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res (2010) 0.97
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res (2009) 0.97
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign. Biophys J (2012) 0.97
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Res (2007) 0.97
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J Phys Chem B (2012) 0.96
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B (2008) 0.96
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Novel evolutionary lineages revealed in the Chaetothyriales (fungi) based on multigene phylogenetic analyses and comparison of its secondary structure. PLoS One (2013) 0.95
The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK. Protein Sci (2005) 0.94
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J Comput Aided Mol Des (2006) 0.94
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B (2008) 0.93
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods (2013) 0.92
Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. J Phys Chem B (2007) 0.91
Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res (2012) 0.91
Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings. J Phys Chem B (2009) 0.91
Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys (2010) 0.90
DNA deformability at the base pair level. J Am Chem Soc (2004) 0.90
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J Comput Aided Mol Des (2011) 0.90
Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes. J Am Chem Soc (2004) 0.89
Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids. J Am Chem Soc (2006) 0.89
Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study. J Phys Chem B (2013) 0.89
Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene. Small (2010) 0.89
Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. J Phys Chem A (2005) 0.89
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys (2012) 0.87
Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations. J Phys Chem B (2005) 0.87
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res (2007) 0.87
Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition. J Phys Chem B (2012) 0.87
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation. Protein Sci (2007) 0.87
Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20. J Mol Biol (2010) 0.87
The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J Chem Theory Comput (2011) 0.86
Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J Chem Theory Comput (2012) 0.86
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations. Chemistry (2006) 0.86
Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions. ACS Nano (2013) 0.86
Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties. Phys Chem Chem Phys (2014) 0.86
Behavior of human cytochromes P450 on lipid membranes. J Phys Chem B (2013) 0.86
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J Phys Chem B (2011) 0.86
On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology. J Phys Chem B (2010) 0.84
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J Phys Chem A (2011) 0.84
Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations. Biochim Biophys Acta (2010) 0.84
Thiofluorographene-hydrophilic graphene derivative with semiconducting and genosensing properties. Adv Mater (2015) 0.83
Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations. J Phys Chem B (2009) 0.83
Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers (2007) 0.83
ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece. Biochim Biophys Acta (2009) 0.83