Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
Computer Modeling of Chemical Reactions in Enzymes and Solutions
- A. Warshel
- 1 November 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…
Advances in methods and algorithms in a modern quantum chemistry program package.
- Y. Shao, L. F. Molnar, M. Head‐Gordon
- ChemistryPhysical Chemistry, Chemical Physics - PCCP
- 4 July 2006
Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
Computer simulation of protein folding
A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding and succeeds in ‘renaturing’ bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule.
Electrostatic basis for enzyme catalysis.
What are the dielectric “constants” of proteins and how to validate electrostatic models?
This review considers the meaning of the protein dielectric constants and the ways to determine their optimal values and introduces a discriminative benchmark that only includes residues whose pKa values are shifted significantly from their values in water.
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Detailed benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset methods for intermolecular interactions, and tests of the accuracy of implicit solvation models are provided.
Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches
One of the most direct benchmarks for electrostatic models of macromolecules is provided by the pKa's of ionizable groups in proteins. Obtaining accurate results for such a benchmark presents a major…
Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites*
- A. Warshel
- BiologyJournal of Biological Chemistry
- 16 October 1998
This review uses energy considerations and the results of computational studies to clarify open questions about enzyme catalysis.