Martin Karplus

The structural enzymology of proton-transfer reactions

The simplest chemical transformations in metabolism are the proton transfer reactions exemplified by certain isomerases and racemases. We have been studying three such enzymes t...

Contact Electron-Spin Coupling of Nuclear Magnetic Moments

The valence-bond theory for the contact electron-spin coupling of nuclear magnetic moments is used to calculate the proton-proton, proton-fluorine, and fluorine-fluorine couplin...

<b>Vicinal Proton Coupling in Nuclear Magnetic Resonance</b>

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVicinal Proton Coupling in Nuclear Magnetic ResonanceMartin. KarplusCite this: J. Am. Chem. Soc. 1963, 85, 18, 2870–2871Publication D...

CHARMM: The biomolecular simulation program

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades ...

A method for determining reaction paths in large molecules: Application to myoglobin

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems....

Molecular dynamics simulations of biomolecules

Dynamics of folded proteins

Molecular dynamics and protein function

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exp...

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibit...

Deformable stochastic boundaries in molecular dynamics

A new approach to studying localized chemical events in condensed phases is developed. The approach provides a simple and convenient method for reducing the total number of solv...

The missing link between thermodynamics and structure in F ₁ -ATPase

F 1 F o -ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F 1 of the F 1 F o complex, F 1 -ATPase, has the ability to...

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase11Edited by A. R. Fersht

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.

Conformational potentials of sidechains in the bovine pancreatic trypsin inhibitor have been studied with an empirical energy function. Calculated minimumenergy positions are in...

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed t...

Stochastic boundary conditions for molecular dynamics simulations of ST2 water