| scholarly article | Q13442814 |
| P50 | author | Darrin M York | Q85376011 |
| Haoyuan Chen | Q88992365 | ||
| P2093 | author name string | Barbara L Golden | |
| Timothy J Giese | |||
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| Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations | Q35537362 | ||
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| Cobalt hexammine inhibition of the hammerhead ribozyme | Q74311737 | ||
| The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA | Q77646670 | ||
| Mechanisms of Ribozyme-Mediated RNA Cleavage | Q77646675 | ||
| NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme | Q81056020 | ||
| Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes | Q84714735 | ||
| Electrophilic assistance to the cleavage of an RNA model phopshodiester via specific and general base-catalyzed mechanisms | Q84997165 | ||
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| Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. | Q35952771 | ||
| The structure-function dilemma of the hammerhead ribozyme | Q36115496 | ||
| Hammerhead ribozymes: importance of stem-loop II for activity | Q36444559 | ||
| Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. | Q36455539 | ||
| Role of pK(a) of nucleobases in the origins of chemical evolution | Q36474674 | ||
| Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis | Q36561838 | ||
| Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids | Q36604456 | ||
| A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations | Q36634357 | ||
| Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue | Q36638679 | ||
| ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. | Q36766916 | ||
| Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation | Q36874094 | ||
| Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme | Q36909656 | ||
| Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation | Q36997163 | ||
| Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation | Q37004094 | ||
| Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation | Q37010636 | ||
| Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry | Q37252921 | ||
| Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation | Q37275350 | ||
| Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations | Q37323544 | ||
| Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions | Q37649459 | ||
| Nucleic acid catalysis: metals, nucleobases, and other cofactors | Q38204496 | ||
| Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity | Q38314474 | ||
| A kinetic and thermodynamic analysis of cleavage site mutations in the hammerhead ribozyme | Q38348527 | ||
| Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles | Q38389887 | ||
| Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations | Q38636305 | ||
| A re-investigation of the thio effect at the hammerhead cleavage site | Q39726744 | ||
| Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate | Q41703953 | ||
| Characterization of a native hammerhead ribozyme derived from schistosomes | Q41874437 | ||
| Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations | Q41930764 | ||
| Role of divalent metal ions in the hammerhead RNA cleavage reaction | Q41963110 | ||
| The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme | Q42021708 | ||
| The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements | Q42353427 | ||
| Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme | Q42846412 | ||
| A stability concept for metal ion coordination to single-stranded nucleic acids and affinities of individual sites | Q43126489 | ||
| Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? | Q43541902 | ||
| A mechanistic comparison of the Varkud satellite and hairpin ribozymes | Q43920666 | ||
| Probing general base catalysis in the hammerhead ribozyme | Q44891143 | ||
| Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. | Q46037009 | ||
| Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site | Q46504044 | ||
| RNA catalysis | Q46726319 | ||
| P433 | issue | 24 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | ribozyme | Q205858 |
| P304 | page(s) | 2985-2994 | |
| P577 | publication date | 2017-06-12 | |
| P1433 | published in | Biochemistry | Q764876 |
| P1476 | title | Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations | |
| P478 | volume | 56 |
| Q58096148 | Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations |
| Q92784376 | Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme |
| Q90070189 | Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution |
| Q91995156 | Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme |
| Q48516878 | Evidence of a General Acid/Base Catalysis Mechanism in the 8-17 DNAzyme |
| Q64068336 | RNA Back and Forth: Looking through Ribozyme and Viroid Motifs |
| Q47235409 | RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. |
| Q48152614 | Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis |
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