Computation based on molecular models is playing an increasingly important role in
biology, biological chemistry, and biophysics. Since only a very limited number of properties …

Protein–protein interactions are vital to biological processes, but the shape and size of their
interfaces make them hard to target using small molecules. Cyclic peptides have shown …

We describe the development, current features, and some directions for future development
of the Amber package of computer programs. This package evolved from a program that was …

Estimating protein–protein interaction energies is a very challenging task for current
simulation protocols. Here, absolute binding free energies are reported for the complex H …

Temperature coefficients have been measured by 2D NMR methods forthe amide and CαH
proton chemical shifts in two globularproteins, bovine pancreatic trypsin inhibitor and hen …

Correlated motions in biomolecules are often essential for their function, eg, allosteric signal
transduction or mechanical/thermodynamic energy transport. Because correlated motions in …

Multiple molecular dynamics (MD) simulations of crambin with different initial atomic
velocities are used to sample conformations in the vicinity of the native structure. Individual …

A 100 ns molecular dynamics simulation of penta‐alanine in explicit water is performed to
study the reversible folding and unfolding of the peptide. Employing a standard principal …

Molecular interactions are essential for regulation of cellular processes from the formation of
multi-protein complexes to the allosteric activation of enzymes. Identifying the essential …

Principal component analysis of molecular dynamics simulations is a popular method to
account for the essential dynamics of the system on a low-dimensional free energy …