To obtain an ensemble structure of the ubiquitin dimer, we performed rigid-body simulated annealing calculations by refining against the intermolecular PRE rates.
DOI: http://dx.doi.org/10.7554/eLife.05767.014 To characterize the closed-state structure of ligand-free K63-Ub2, we performed rigid-body simulated annealing refinement against the inter-subunit PREs.
To confirm this model, we performed rigid-body modeling against the R0RBR pUb SAXS data using the structures of the Parkin R0RBR module (Trempe et al, 2013) and pUb (Wauer et al, 2015b), while maintaining a short distance between Ser65 in pUb and His302/Arg305.
If you don't put me on the team, I'm going down there to skate against you guys.' " When the Z-Boys first competed professionally at the Del Mar Nationals in 1975, it mystified other skateboarders, who were performing rigid gymnastic maneuvers from the 1960s.
A better approach is to perform rigid registration to remove the effects of drift, followed by non-rigid registration to remove the effects of short period instabilities in the scanning system [41, 42].
It was initially designed to perform rigid molecular docking in order to ultimately pose a ligand in the receptor site by combining the Divide and Conquer linear-scaling quantum-chemistry method with a genetic algorithm (GA).
The term partial Procrustes specifically refers to the subset of methods that maintain scale, i.e. those approaches that only perform rigid body transformations [43].
Automated software written in C++ was used to perform rigid or nonrigid registration (depending on atrial wall overlap) between the segmented magnetic resonance angiography (MRA) and LGE surfaces.
The first fragment-based comparison method was proposed by Remington and Mathews, which performs rigid body superposition of fixed length backbone fragments from individual proteins (Matthews et al., 1981).
It is standard practice in our unit that patients who have undergone a clam enterocystoplasty are followed up yearly by performing rigid cystoscopy and biopsy of the urothelium at the enterovesical anastomosis.
