Conformational sampling structural ensembles

On the other hand, the extraction of the structural ensemble from the molecular dynamics trajectories likely generates a fluctuation along the starting structure unless the conformational sampling is assessed correctly. In the case of ubiquitin, the X-ray structure could be a good approximation of a global minimum of the solution structure. 

The most common docking technique that attempts to account for protein flexibility uses multiple protein stmctures. The ensemble of structures is expected to represent the range of conformations sampled by the protein and has the benefit of being able to evaluate both small and large conformational changes. The molecular docking is repeated for each individual protein conformation, which... 

We note that the RISM equations, a large set of stiff, nonlinear simultaneous equations, must be solved for all the conformations sampled. However, we employ our robust algorithm [13] that is over two orders of magnitude faster than the conventional one. As a result, the ensemble-averaged structure of the solvent, which is in equilibrium with the pep-... 

Determination of Structural Ensembles from NMR Data Conformational Sampling and Probability Assessment... 

The importance of treating the NMR observables and from them derived parameters as ensembles over relevant time scales rather than individual conformers is highlighted by Angyan and Gaspari who discuss several MD simulation techniques to interpret the structural and dynamical data from NMR. Internal dynamics in proteins take place at several different time scales. It is therefore important to sample the ensembles covering the specific time scales. 

The CBMC algorithm greatly improves the conformational sampling for molecules with articulated structure and increases the efficiency of chain insertions (required for the calculation of chemical potentials, grand-canonical, and Gibbs ensemble simulations) by several orders of magnitude. To make these simulations more efficient and to use this technique for branched molecules, several extensions are needed ... 

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