Molecular-dynamics simulation methods for macromolecular crystallography.

ABSTRACT: It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein-solvent interface. To address this limitation, a set of MD-MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room tem

SUBMITTER: Wych DC 

PROVIDER: S-EPMC9815100 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature