Paper Citing NAMD - Abstract
Park, Sanghyun; Bardhan, Jaydeep P.; Roux, Benoit; Makowski, Lee
Simulated x-ray scattering of protein solutions using explicit-solvent models
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 134114, APR 7 2009
X-ray solution scattering shows new promise for the study of protein structures, complementing crystallography and nuclear magnetic resonance. In order to realize the full potential of solution scattering, it is necessary to not only improve experimental techniques but also develop accurate and efficient computational schemes to relate atomistic models to measurements. Previous computational methods, based on continuum models of water, have been unable to calculate scattering patterns accurately, especially in the wide-angle regime which contains most of the information on the secondary, tertiary, and quaternary structures. Here we present a novel formulation based on the atomistic description of water, in which scattering patterns are calculated from atomic coordinates of protein and water. Without any empirical adjustments, this method produces scattering patterns of unprecedented accuracy in the length scale between 5 and 100 A, as we demonstrate by comparing simulated and observed scattering patterns for myoglobin and lysozyme.
