Published in J Phys Chem B on November 08, 2011
General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J Am Chem Soc (2012) 1.05
Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. J Am Chem Soc (2015) 0.93
Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. J Am Chem Soc (2013) 0.83
The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys Chem Chem Phys (2015) 0.79
Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage. Biopolymers (2015) 0.78
Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis. RNA Biol (2013) 0.75
Molecular modeling of nucleic acid structure: energy and sampling. Curr Protoc Nucleic Acid Chem (2001) 0.75
Pressure modulates the self-cleavage step of the hairpin ribozyme. Nat Commun (2017) 0.75
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (2017) 0.75
Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme. Biophys Chem (2017) 0.75
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter (1988) 93.32
Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys (1988) 39.03
Quantum mechanical continuum solvation models. Chem Rev (2005) 10.95
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol (1976) 9.91
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature (2001) 4.59
Electrostatic basis for enzyme catalysis. Chem Rev (2006) 4.35
Transition state stabilization by a catalytic RNA. Science (2002) 2.73
Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev (1999) 2.58
Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J Am Chem Soc (2004) 2.51
Continuous surface charge polarizable continuum models of solvation. I. General formalism. J Chem Phys (2010) 2.40
Mechanisms and free energies of enzymatic reactions. Chem Rev (2006) 2.25
Structure and function of the hairpin ribozyme. J Mol Biol (2000) 1.98
Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. Biochemistry (2003) 1.94
Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucleic Acids Res (1990) 1.80
Comparative enzymology and structural biology of RNA self-cleavage. Annu Rev Biophys (2009) 1.71
Catalytic strategies of self-cleaving ribozymes. Acc Chem Res (2008) 1.67
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J (2001) 1.65
Role of an active site adenine in hairpin ribozyme catalysis. J Mol Biol (2005) 1.62
Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue. J Mol Biol (2004) 1.57
Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res (1997) 1.55
The hairpin ribozyme: structure, assembly and catalysis. Curr Opin Chem Biol (1998) 1.52
Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev (2010) 1.52
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chemistry (2006) 1.46
Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry (2006) 1.41
Autolytic processing of a phosphorothioate diester bond. Nucleic Acids Res (1988) 1.39
Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers (2004) 1.39
Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc Natl Acad Sci U S A (2006) 1.34
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA (2007) 1.27
Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res (1986) 1.24
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. J Am Chem Soc (2008) 1.23
Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis. Chem Biol (2002) 1.21
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc (2009) 1.20
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
Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme. Nat Chem Biol (2009) 1.11
Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms. J Chem Theory Comput (2007) 1.10
The origins of RNA catalysis in ribozymes. Trends Biochem Sci (2003) 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
Ribozyme catalysis revisited: is water involved? Mol Cell (2007) 1.05
Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. J Phys Chem B (2006) 1.05
Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory. Biochemistry (2006) 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
The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine. J Biol Chem (2011) 1.01
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. RNA (2008) 1.00
Catalytic importance of a protonated adenosine in the hairpin ribozyme active site. Biochemistry (2010) 0.98
Identification of an imino group indispensable for cleavage by a small ribozyme. J Am Chem Soc (2009) 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
Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification. J Phys Chem B (2005) 0.95
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Functional analysis of hairpin ribozyme active site architecture. J Biol Chem (2007) 0.91
Density functional theory investigation on the mechanism of the hepatitis delta virus ribozyme. J Phys Chem B (2007) 0.90
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochem Biophys Res Commun (2008) 0.87
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
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins (2008) 0.83
Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme. J Am Chem Soc (2002) 0.83
Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes. J Phys Chem B (2011) 0.80
Theoretical examination of Mg(2+)-mediated hydrolysis of a phosphodiester linkage as proposed for the hammerhead ribozyme. J Am Chem Soc (2003) 0.80
Correlating structural dynamics and function in single ribozyme molecules. Science (2002) 5.16
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics (2006) 4.11
Molecular robots guided by prescriptive landscapes. Nature (2010) 3.23
Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. Chem Rev (2012) 3.19
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (2007) 2.49
RNA dynamics: it is about time. Curr Opin Struct Biol (2008) 2.31
Single-molecule transition-state analysis of RNA folding. Proc Natl Acad Sci U S A (2003) 2.31
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
Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc Natl Acad Sci U S A (2004) 2.11
Purification and functional reconstitution of monomeric mu-opioid receptors: allosteric modulation of agonist binding by Gi2. J Biol Chem (2009) 1.59
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J (2006) 1.54
Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting". Proc Natl Acad Sci U S A (2007) 1.48
Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nat Struct Mol Biol (2010) 1.45
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
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
Trans-acting glmS catalytic riboswitch: locked and loaded. RNA (2007) 1.32
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles. Biotechnol J (2007) 1.31
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res (2008) 1.30
Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry (2002) 1.27
Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry (2002) 1.26
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform (2013) 1.26
Analysis of complex single-molecule FRET time trajectories. Methods Enzymol (2010) 1.23
Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core. Biochemistry (2003) 1.22
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
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA (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
Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence. Biochemistry (2003) 1.15
Focus on function: single molecule RNA enzymology. Biopolymers (2007) 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
Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nat Struct Mol Biol (2013) 1.11
The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry (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
Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J Mol Biol (2008) 1.08
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
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res (2011) 1.06
Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme. J Mol Biol (2004) 1.05
Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc (2011) 1.05
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
Fluorescent energy transfer readout of an aptazyme-based biosensor. Methods Mol Biol (2006) 1.02
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr Drug Metab (2012) 1.02
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res (2011) 1.02
Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys (2009) 1.01
Flexible casting of modular self-aligning microfluidic assembly blocks. Lab Chip (2011) 1.00
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res (2013) 0.98
Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core. Biochemistry (2006) 0.97
Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum. RNA (2007) 0.97
High-energy chemistry of formamide: a simpler way for nucleobase formation. J Phys Chem A (2014) 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
Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO Rep (2012) 0.96
RNA chaperones stimulate formation and yield of the U3 snoRNA-Pre-rRNA duplexes needed for eukaryotic ribosome biogenesis. J Mol Biol (2009) 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
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J Phys Chem B (2012) 0.96
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. RNA (2010) 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
Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. J Am Chem Soc (2011) 0.94
Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophys J (2006) 0.94
Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev (2014) 0.94
DNA-cholesterol barges as programmable membrane-exploring agents. ACS Nano (2014) 0.93
Metal ions: supporting actors in the playbook of small ribozymes. Met Ions Life Sci (2011) 0.93
RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer. J Am Chem Soc (2003) 0.92
Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. RNA (2012) 0.92
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods (2013) 0.92
Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme. Biochemistry (2004) 0.90
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
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
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
On the road from formamide ices to nucleobases: IR-spectroscopic observation of a direct reaction between cyano radicals and formamide in a high-energy impact event. J Am Chem Soc (2012) 0.90
Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA (2008) 0.90
A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. RNA (2002) 0.90
A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P. J Mol Biol (2010) 0.89
High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun (2013) 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
Single molecule fluorescence control for nanotechnology. J Nanosci Nanotechnol (2005) 0.88