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Using these RDCs, an ensemble was determined using the SAS approach and a grid search was performed over sterically allowed conformations.
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As mentioned, a structural ensemble of low conformational energy IsdBN1 conformers was determined using a standard simulated annealing protocol of CYANA 2.1 followed by "water refinement" of selected conformers using the program AMBER9.
Exon information was determined using annotations from the UCSC Known Genes and Ensemble databases (mouse, version mm8) and all transcripts were collapsed to match to Affy ID annotations[32].
The structure of I was determined using molecular replacement and PHASER (McCoy et al., 2005) using an ensemble comprising PDB accession codes 1OPL, 1OPK, and 2FO0.
eBoldface names and architectures indicate models in which ensemble classifications were determined using the averaging method.
The localization labels of the cell were determined using our ensemble classifiers.
To determine the molecular details of the structures giving rise to the PRE NMR data, ensembles of structures compatible with the PRE-derived distances were determined using replica-averaged restrained MD (PRE-RMD) simulations.
Phase equilibria of nine n-alkane/nitrogen mixtures (each at various temperatures) are determined using Monte Carlo simulations in the grand canonical ensemble.
The excess chemical potentials have been determined using Widom's test-particle insertion method considering an ensemble of microstructures generated by Monte Carlo calculations.
The corrected canonical ensemble was determined by performing a free energy weighting protocol.
The size of the null ensemble is determined by the input choice of using either the fixed or adaptive ensemble size (see Section 4.5).
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