| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcc/RostaWBH09 |
| P356 | DOI | 10.1002/JCC.21312 |
| P932 | PMC publication ID | 3098573 |
| P698 | PubMed publication ID | 19462398 |
| P5875 | ResearchGate publication ID | 24446478 |
| P50 | author | Gerhard Hummer | Q41049131 |
| Edina Rosta | Q56654431 | ||
| Henry Woodcock | Q74214209 | ||
| P2093 | author name string | Bernard R Brooks | |
| P2860 | cites work | A general two-metal-ion mechanism for catalytic RNA | Q24562157 |
| Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis | Q24649179 | ||
| Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription | Q27648911 | ||
| Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity | Q29615987 | ||
| Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis | Q29619064 | ||
| On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions | Q30355668 | ||
| A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. | Q30483153 | ||
| Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems | Q30485543 | ||
| Escaping free-energy minima | Q34151010 | ||
| Human RNase H1 Uses One Tryptophan and Two Lysines to Position the Enzyme at the 3′-DNA/5′-RNA Terminus of the Heteroduplex Substrate | Q34264646 | ||
| Local elevation: a method for improving the searching properties of molecular dynamics simulation. | Q34309917 | ||
| Type II restriction endonucleases: structure and mechanism | Q34555997 | ||
| Advances in methods and algorithms in a modern quantum chemistry program package. | Q34556469 | ||
| Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism. | Q34801870 | ||
| Models for biological phosphoryl transfer | Q35692118 | ||
| Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies. | Q36982357 | ||
| On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution | Q43537248 | ||
| On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins | Q44955947 | ||
| The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase | Q45070165 | ||
| Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions | Q46358954 | ||
| The role of metal ions in phosphate ester hydrolysis. | Q50104440 | ||
| A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. | Q51629784 | ||
| Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase | Q56991623 | ||
| Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis | Q59345701 | ||
| Reactivity of alcohols toward the phosphoenzyme intermediate in the protein-tyrosine phosphatase-catalyzed reaction: probing the transition state of the dephosphorylation step | Q71506677 | ||
| Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations | Q79864597 | ||
| Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms | Q80444747 | ||
| P433 | issue | 11 | |
| P304 | page(s) | 1634-1641 | |
| P577 | publication date | 2009-08-01 | |
| P1433 | published in | Journal of Computational Chemistry | Q3186908 |
| P1476 | title | Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H | |
| P478 | volume | 30 |
| Q36520871 | Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design |
| Q42682544 | Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping |
| Q84619803 | Atomistic details of the associative phosphodiester cleavage in human ribonuclease H |
| Q34402463 | Calcium inhibition of ribonuclease H1 two-metal ion catalysis |
| Q30500960 | Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations |
| Q30569983 | Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. |
| Q36120580 | Characterization of a dynamic string method for the construction of transition pathways in molecular reactions |
| Q39204260 | Charting molecular free-energy landscapes with an atlas of collective variables. |
| Q40454946 | Computational delineation of the catalytic step of a high-fidelity DNA polymerase. |
| Q30581942 | Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain |
| Q30376837 | Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter. |
| Q35734759 | Convergence and error estimation in free energy calculations using the weighted histogram analysis method |
| Q30804652 | Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. |
| Q34214770 | Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions |
| Q36315952 | Energetics and dynamics of proton transfer reactions along short water wires. |
| Q24621754 | ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation |
| Q33654266 | Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site |
| Q37312913 | Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study |
| Q54768076 | Hydrolysis of the damaged deoxythymidine glycol nucleoside and comparison to canonical DNA. |
| Q38536147 | Mechanisms of DNA Transposition |
| Q36616106 | Molecular simulations of RNA 2'-O-transesterification reaction models in solution |
| Q37183610 | Multiensemble Markov models of molecular thermodynamics and kinetics. |
| Q91255564 | Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide |
| Q64984185 | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms. |
| Q38223681 | Quantum mechanical modeling: a tool for the understanding of enzyme reactions |
| Q45156666 | Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency |
| Q34125552 | Recent developments in methods for identifying reaction coordinates |
| Q33882128 | Sampling long time scale protein motions: OSRW simulation of active site loop conformational free energies in formyl-CoA:oxalate CoA transferase |
| Q49118107 | Umbrella integration with higher-order correction terms. |
| Q42037579 | Unlocking the atomic-level details of amyloid fibril growth through advanced biomolecular simulations |
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