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An SVD analysis was performed to determine the optimal alignment tensor for molecular ensembles generated at each acceleration level (37).
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Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures.
A preliminary free-energy landscape is first calculated from a conformation ensemble generated by a multicanonical molecular dynamics simulation with the GB model.
(B ) Centers of HPr structures, shown as blue spheres, in the encounter complex ensemble generated by the PIPER docking program.
These five RDCs also did not fit those generated from the X-ray crystal structure and from the MD-generated molecular ensembles.
To generate a set of molecular ensembles of the thermal folding of TC5b, we equilibrated 32 replicas of TC5b in explicit water at 273 363 K, corresponding to the temperature range of experimentally measured thermal stability of TC5b [28].
Mesoscopic simulation targets large molecular ensembles which represent up to millions of molecules.
Rather, they have the manner of an African or Indian ensemble generating a mood.
Molecular images generated using the CH5M3D library.
In order to quantify collective properties of the molecular ensemble, we calculate the consensus sequence of the population.
By construction, the three ensembles were generated so that A and C would both be more similar to ensemble B than to each other.
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