… exists in the simultaneous refinement of structures, for … In such a refinement, all observations
would be fit simultaneously, … relationships among the measured sets of structure factors. …

… To achieve this goal, we report an integrative modeling approach to simultaneously determine
structure and dynamics of macromolecular systems from cryo-electron microscopy density …

… This expression is similar to the one used by Tolman for calculating a refined structure matrix
given a structural model B (0) and an alignment tensor <A>. The first term of the right side of …

… their own merits and the shortcomings simultaneously, highlighting that using multiple
energy functions in protein structure refinement can be more effective than using a single one. …

Recent studies have shown that explicit solvent molecular dynamics (MD) simulation followed
by structural averaging can consistently improve protein structure models. We find that …

… If a potential solvent site was too close to a previously identified site to permit both sites to
be occupied simultaneously, the new site was flagged so that restraints against close contacts …

… The algorithm used for this refinement allows for the simultaneous restraint on bond distances
and … The refined structure of SGPA differs from ideal bond lengths by an overall root-mean-…

… (A) Comparison of the small subunit maps reconstructed from conventional SPA procedure
(left in grey), LO-refinement procedure with the simultaneous parameter-searching strategy (…

… This possibility is also very difficult to allow for during structure refinement, as the necessary
information cannot be known a priori and is in general too complex to be determined from …

… ab-initio, a protocol for simultaneous docking and de-novo folding … structural representation
of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously …