Paper Citing NAMD - Abstract
Shang, Zhiguo; Sigworth, Fred J.
Hydration-layer models for cryo-EM image simulation
JOURNAL OF STRUCTURAL BIOLOGY, 180:10-16, OCT 2012
To compare cryo-EM images and 3D reconstructions with atomic structures in a quantitative way it is essential to model the electron scattering by solvent (water or ice) that surrounds protein assemblies. The most rigorous method for determining the density of solvating water atoms for this purpose has been to perform molecular-dynamics (MD) simulations of the protein-water system. In this paper we adapt the ideas of bulk-water modeling that are used in the refinement of X-ray crystal structures to the cryo-EM solvent-modeling problem. We present a continuum model for solvent density which matches MD-based results to within sampling errors. However, we also find that the simple binary-mask model of Jiang and Brunger (1994) performs nearly as well as the new model. We conclude that several methods are now available for rapid and accurate modeling of cryo-EM images and maps of solvated proteins. (C) 2012 Elsevier Inc. All rights reserved.
