Computer Modeling of Chemical Reactions in Enzymes and Solutions
@inproceedings{Warshel1991ComputerMO, title={Computer Modeling of Chemical Reactions in Enzymes and Solutions}, author={Arieh Warshel}, year={1991} }
Basic Principles of Chemical Bonding. Chemical Reactions in the Gas Phase and in Simple Solvent Models. Chemical Reaction in All--Atom Solvent Models. Potential Surfaces and Simulations of Macromolecules. Modeling Reactions in Enzymes: An Introduction. General Acid Catalysis and Electrostatic Stabilization in the Catalytic Reaction of Lysozyme. Serine Proteases and the Examination of Different Mechanistic Options. Simulating Metalloenzymes. How Do Enzymes Really Work? Index.
935 Citations
Computational enzymology.
- Chemistry, BiologyChemical communications
- 2010
Computer simulations and modelling can provide detailed, atomic-level insight into the fundamental mechanisms of biological catalysts and potential practical applications include interpretation of experimental data, catalyst design and drug development.
Computer Simulation of the Triosephosphate Isomerase Catalyzed Reaction (*)
- Chemistry, BiologyThe Journal of Biological Chemistry
- 1996
The calculations clearly demonstrate the important catalytic effects associated with stabilization of charged high energy intermediates and reduction of reorganization energy, which are likely to be general principles of enzyme catalyzed charge transfer and separation reactions.
Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?
- Chemistry, Biology
- 2002
Although the preorganization free energy contains a large entropic contribution, entropy effects on going from the enzyme−substrate noncovalent complex to the transition state for the reaction are expected to be generally small and not very different in enzyme and in solution.
Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase.
- Chemistry, PhysicsCurrent opinion in structural biology
- 2004
How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations
- PhysicsScience
- 2004
A framework for understanding the effects of lowering of the activation free energy and changes in the generalized transmission coefficient on enzyme catalysis is presented, and the contributions of the different factors are identified and quantified by computer simulations.
Simulation of chemical reactions in solution by a combination of classical and quantum mechanical approach
- Chemistry, Physics
- 1995
Simulating enzyme reactions: Challenges and perspectives
- Computer ScienceJ. Comput. Chem.
- 2002
Some of the processes that need to be investigated if enzyme catalysis is to be understood are outlined, the current state‐of‐the‐art in enzyme simulation work is reviewed, and challenges for the future are highlighted.
Computational modeling of enzymatic keto-enol isomerization reactions
- Chemistry
- 2002
Abstract. Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the…
Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions
- Biology, ChemistryBiomolecules
- 2013
In this review, an overview to non-specialists on various enzyme models as well as established computational methods are given and applications to some specific cases are described.
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