Published in J Phys Chem B on March 11, 2010
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
Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput (2011) 0.85
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. J Chem Theory Comput (2012) 0.84
On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies. RNA (2010) 0.79
Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. J Mol Model (2012) 0.78
RNABP COGEST: a resource for investigating functional RNAs. Database (Oxford) (2015) 0.77
Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Res (2013) 0.76
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic Acids Res (2015) 0.76
How Does Mg(2+) Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair. Biophys J (2017) 0.75
Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies. J Mol Model (2017) 0.75
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
DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J (2003) 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
Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers (2007) 1.41
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
Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J (2004) 1.33
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
Ribosomal RNA kink-turn motif--a flexible molecular hinge. J Biomol Struct Dyn (2004) 1.23
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
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure (2006) 1.17
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
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
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
Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys (2009) 1.01
Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs. J Mol Biol (2003) 1.00
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
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Res (2007) 0.97
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
Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Biomol Struct Dyn (2006) 0.93
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B (2008) 0.93
Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: a multifunctional target for antischistosomal therapy. J Mol Graph Model (2008) 0.93
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 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
Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res (2012) 0.91
The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA. J Biol Chem (2002) 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
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
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
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Comput Aided Mol Des (2006) 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
RNA structure and dynamics: a base pairing perspective. Prog Biophys Mol Biol (2013) 0.87
Lack of association of brucellosis resistance with (GT)(13) microsatellite allele at 3'UTR of NRAMP1 gene in Indian zebu (Bos indicus) and crossbred (Bos indicus x Bos taurus) cattle. Vet Microbiol (2005) 0.86
Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput (2011) 0.85
Isolation of two cDNAs encoding MHC-DQA1 and -DQA2 from the water buffalo, Bubalus bubalis. Vet Immunol Immunopathol (2009) 0.85
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
A fluorogenic peptide containing the processing site of human SARS corona virus S-protein: kinetic evaluation and NMR structure elucidation. Chembiochem (2007) 0.84
Structural stability of tandemly occurring noncanonical basepairs within double helical fragments: molecular dynamics studies of functional RNA. J Phys Chem B (2010) 0.83
Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches. J Mol Model (2009) 0.83
Effect of phosphorothioate chirality on the grooves of DNA double helices: a molecular dynamics study. Biopolymers (2004) 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
Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations. J Phys Chem B (2009) 0.83
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment. Biopolymers (2013) 0.83
Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles. J Biomol Struct Dyn (2011) 0.82
Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics. Biopolymers (2008) 0.82
Interactions of the "piano-stool" [ruthenium(II) (eta6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study. J Comput Chem (2009) 0.82
Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J (2012) 0.82
Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA. J Phys Chem B (2007) 0.82
Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+. J Phys Chem B (2007) 0.81
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. BMC Bioinformatics (2011) 0.81
Role of hydrogen bonds in protein-DNA recognition: effect of nonplanar amino groups. J Phys Chem B (2005) 0.81
Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies. J Phys Chem B (2008) 0.81
HD-RNAS: An Automated Hierarchical Database of RNA Structures. Front Genet (2012) 0.81
Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine. J Am Chem Soc (2004) 0.80
Protonation of base pairs in RNA: context analysis and quantum chemical investigations of their geometries and stabilities. J Phys Chem B (2011) 0.80
Theoretical analysis of noncanonical base pairing interactions in RNA molecules. J Biosci (2007) 0.80
Characterization of unfolding mechanism of human lamin A Ig fold by single-molecule force spectroscopy-implications in EDMD. Biochemistry (2014) 0.80
Analysis of stacking overlap in nucleic acid structures: algorithm and application. J Comput Aided Mol Des (2014) 0.80
On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies. RNA (2010) 0.79
Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): evidence for duplication. Vet Immunol Immunopathol (2010) 0.79
Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study. Phys Chem Chem Phys (2014) 0.79
Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family. J Phys Chem B (2007) 0.79
Why pyridine containing pyrido[2,3-d]pyrimidin-7-ones selectively inhibit CDK4 than CDK2: insights from molecular dynamics simulation. J Mol Graph Model (2010) 0.79
Changes in thermodynamic properties of DNA base pairs in protein-DNA recognition. J Biomol Struct Dyn (2010) 0.79
Copper cation interactions with biologically essential types of ligands: a computational DFT study. J Phys Chem A (2006) 0.79