Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc.

ABSTRACT: Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative b

SUBMITTER: Ariz-Extreme I 

PROVIDER: S-EPMC5957342 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature