… of a number of structure refinement methods, evaluating them for optimality (minimization of
Rosetta energy and RMSD from the starting structure simultaneously) and for their influence …

… Although the data sets used in this study are known to be simultaneous, all of the results
described above were generated under weak simultaneity as described in the Methods section. …

… so hard to predict and refine protein structures using molecular simulation even … protein
structure gets within a small enough rms distance from the experimentally determined structure …

… First, the Hamiltonian H0 is not an ideal gas Hamiltonian, and second we wish to optimize
the excluded volume parameters simultaneously with additional parameters governing the …

… the structure determination and refinement of small proteins and … This is followed by
applications to crystallographic refinement of … The simultaneous A ,B restraints could be …

… of protein geometry, resulting in final structures that … structures generated only with traditional
restraints can be successfully refined using traditional and PCS restraints simultaneously…

… This paper presents a rapid refinement procedure capable of … all parts of the structure are
refined simultaneously in a general … significantly to the refined protein conformation. Hydrogen …

… For refinement, a set of n simultaneous linear equations are involved, analogous to the
normal equations of least squares. Their right-hand sides are the slopes of the difference map at …

… j and jFÀj, and the associated calculated model structure factors into structure refinement.
The function allows for the simultaneous refinement of the heavy-atom and model parameters …

… 'idealized' starting atomic coordinates of yeast phenylalanine tRNA by connecting the
stereochemically ideal constrained groups with restrained distances, then simultaneously …