Structural dynamics of water and its hydrogen-bonding networks play an important role in
enzyme function via the transport of protons, ions, and substrates. To gain insights into these …

Water often plays a key role in protein structure, molecular recognition, and mediating
protein–ligand interactions. Thus, free energy calculations must adequately sample water motions, …

Enzymes populate ensembles of structures necessary for catalysis that are difficult to
experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray …

This review article provides an overview of structurally oriented, experimental datasets that
can be used to benchmark protein force fields, focusing on data generated by nuclear …

Molecular-dynamics (MD) simulations have contributed substantially to our understanding
of protein structure and dynamics, yielding insights into many biological processes including …

To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD)
simulations of a periodic 2× 2× 2 supercell of staphylococcal nuclease. We used the resulting …

Molecular-dynamics (MD) simulations of protein crystals enable the prediction of structural
and dynamical features of both the protein and the solvent components of macromolecular …

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance
macromolecular crystallography (MX) studies. Historically, protein crystal structures have been …

1 ABSTRACT Water often plays a key role in protein structure, molecular recognition, and
mediating protein-ligand interactions. Thus, free energy calculations must adequately sample …

A fixed-charge MD force field by definition requires a compromise in the electrostatic model
used. For example, amino acids in the hydrophobic core of a protein are modeled with the …