| scholarly article | Q13442814 |
| P50 | author | Qiang Cui | Q87635489 |
| P2093 | author name string | Daniel Roston | |
| Victor Ovchinnikov | |||
| Darren Demapan | |||
| Xiya Lu | |||
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| Origins of catalysis by computationally designed retroaldolase enzymes | Q33740304 | ||
| The rotary machine in the cell, ATP synthase | Q33925462 | ||
| Structural mechanism of muscle contraction. | Q33953597 | ||
| Kinetic resolution of a conformational transition and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin II mutant containing a single tryptophan residue | Q34095252 | ||
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| Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase | Q34165729 | ||
| On the Mechanism of ATP Hydrolysis in F1-ATPase | Q34183062 | ||
| Unraveling the mystery of ATP hydrolysis in actin filaments | Q34282562 | ||
| The physics of molecular motors | Q34285697 | ||
| Emerging complex pathways of the actomyosin powerstroke. | Q34348406 | ||
| Early stages of energy transduction by myosin: roles of Arg in switch I, of Glu in switch II, and of the salt-bridge between them | Q34385871 | ||
| Extreme electric fields power catalysis in the active site of ketosteroid isomerase | Q34454777 | ||
| Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. | Q34699313 | ||
| Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism | Q34752895 | ||
| Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications | Q35013411 | ||
| Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome | Q35049159 | ||
| Oxygen exchange in the gamma-phosphoryl group of protein-bound ATP during Mg2+-dependent adenosine triphosphatase activity of myosin | Q35083724 | ||
| Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase | Q35127441 | ||
| Comparative laboratory evolution of ordered and disordered enzymes. | Q35351471 | ||
| A conformational transition in the myosin VI converter contributes to the variable step size | Q35556327 | ||
| Biomolecular motors: the F1-ATPase paradigm | Q35749528 | ||
| Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling | Q35758716 | ||
| Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations | Q36279979 | ||
| The molecular mechanism of muscle contraction. | Q36288552 | ||
| Functional transitions in myosin: formation of a critical salt-bridge and transmission of effect to the sensitive tryptophan. | Q36482746 | ||
| Enzymatic mechanisms of phosphate and sulfate transfer. | Q36559640 | ||
| Enzyme promiscuity: evolutionary and mechanistic aspects. | Q36580808 | ||
| Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations | Q36789334 | ||
| Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications | Q36903666 | ||
| Biomolecular dynamics: order-disorder transitions and energy landscapes | Q36962788 | ||
| Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods | Q37055269 | ||
| Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily | Q37137337 | ||
| QM/MM free energy simulations: recent progress and challenges | Q37194421 | ||
| Directed enzyme evolution: climbing fitness peaks one amino acid at a time | Q37244268 | ||
| Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol | Q37249163 | ||
| Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps | Q37309585 | ||
| Perspective: Quantum mechanical methods in biochemistry and biophysics | Q37341806 | ||
| Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. | Q37372651 | ||
| Quantitative exploration of the molecular origin of the activation of GTPase | Q37409341 | ||
| The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state | Q37438825 | ||
| Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. | Q37579342 | ||
| Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. | Q37691765 | ||
| Structural and functional insights into the Myosin motor mechanism | Q37700646 | ||
| Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications | Q37701717 | ||
| Computational enzyme design | Q38092809 | ||
| Design of protein catalysts | Q38112831 | ||
| Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency? | Q38222399 | ||
| What vibrations tell us about GTPases | Q38242876 | ||
| Advances in quantum simulations of ATPase catalysis in the myosin motor. | Q38501292 | ||
| The proton inventory technique. | Q40078944 | ||
| Parametrization and Benchmark of DFTB3 for Organic Molecules | Q40295934 | ||
| Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths, and bond angles of the GTP ligand induced by the Ras-protein | Q40334259 | ||
| Density functional tight binding: values of semi-empirical methods in an ab initio era. | Q40354891 | ||
| Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center | Q41685643 | ||
| How does GAP catalyze the GTPase reaction of Ras? A computer simulation study | Q41753437 | ||
| BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". | Q41996880 | ||
| Stabilization of the ADP/metaphosphate intermediate during ATP hydrolysis in pre-power stroke myosin: quantitative anatomy of an enzyme | Q42057214 | ||
| DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). | Q42073025 | ||
| Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations | Q43517433 | ||
| Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. | Q45718253 | ||
| Automated discovery of chemically reasonable elementary reaction steps | Q45819255 | ||
| BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". | Q46086268 | ||
| Dynamically controlled protein tunneling paths in photosynthetic reaction centers | Q46131747 | ||
| Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules | Q46612122 | ||
| Proton-coupled electron transfer in molecular electrocatalysis: theoretical methods and design principles | Q46905851 | ||
| Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site | Q47126560 | ||
| Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects | Q47408948 | ||
| The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations | Q47772171 | ||
| P433 | issue | 10 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 1482-1497 | |
| P577 | publication date | 2017-03-01 | |
| P1433 | published in | Biochemistry | Q764876 |
| P1476 | title | Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin | |
| P478 | volume | 56 |
| Q47095034 | Kinesin motility is driven by subdomain dynamics |
| Q89654701 | Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model |
| Q47160816 | Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. |
| Q64953137 | Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. |
| Q90044150 | Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins |
| Q48053683 | Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug-Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies. |
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