No solution was found to satisfy this restraint (data not shown) indicating that the two subunits of a K63-linked diUb cannot be accommodated simultaneously in both Josephin sites.
It is important to note that in this approach it is attempted that all conformations should individually satisfy the restraints.
In these simulations, the experimental restraints are applied to multiple copies, or replicas, of the protein at any given time and the optimization protocol then aims to find ensembles that satisfy the restraints when the distances are back-calculated as an average over the ensemble.
In this way, the simulations were progressively biased toward structures that, on average, satisfy the restraints.
Modeller attempts to satisfy spatial restraints in order to build a target protein structure.
As we are interested only in models that best satisfy the restraints, we select a small fraction of the models representing the very best scoring solutions.
In this way, as the simulation proceeds, the ensemble of structures is progressively biased toward structures that, on average, satisfy the restraints.
As we are interested only in models that best satisfy the restraints, we select the very small fraction of the models representing the very best scoring solutions.
The approach aims to obtain a single structure that satisfies CXMS restraints and has the lowest ROSETTA energy score, and is suited for characterizing stable complex structures.
To build models, MODELLER satisfies spatial restraints derived from the sequence alignment between the target and its templates.
The final structure is presented by MODELLER (Sali and Blundell 1993) using a program that creates a probability density function using geometric criteria that satisfies spatial restraints within the query sequence in comparison to solved structures.
