Similar to the molten core dynamics for proline isomerase, the structure ensembles generated by the ensemble refinement method revealed specific core dynamics for HIV protease, in particular a conformational exchange that is likely functionally relevant.
Moreover, the ensembles generated by the other distance measures showed a better performance of CVAA than Ward and graph-based consensus clustering methods using both criteria.
Rev. 54 (2001) 1] based on the theory of functions of random variables and Green's functions is used to demonstrate the dependence of effective elastic moduli of fiber reinforced composites on the fiber radial distribution functions as estimated from measured experimental data as well as from the ensembles generated by the proposed method.
Rev., (2001a), 54, 1 47) based on the theory of functions of random variables and Green's functions is used for demonstration of the dependence of effective elastic moduli of fiber composites on the radial distribution functions estimated from the real experimental data as well as from the ensembles generated by the method proposed.
We have illustrated this problem by performing both implicit and explicit solvent simulations of five galectin-3 complexes [30]: Ensembles generated by the different solvent models are rather different with root-mean-square deviations of 1.2 – 1.4 Å and the quality of the predicted affinities changes significantly.
To speed up the calculation, the minimization of the conformational ensemble generated by OMEGA can be parallelized.
A preliminary free-energy landscape is first calculated from a conformation ensemble generated by a multicanonical molecular dynamics simulation with the GB model.
Finally, thermodynamic properties evaluated from the ensembles generated by MD can help to quantify the corresponding structural observations.
Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures.
There are, however, cases where several equivalent reference structures are available, e.g. structural ensembles generated by NMR, crystal structures with multiple copies of the protein in the asymmetric unit (non-crystallographic symmetry) (e.g. target T603 in CASP9), or independently determined X-ray structures for the same protein at different experimental conditions.
