RMSD values (Å) for LBMC simulation trajectories, from Figure 4. RMSD values (Å) for MD simulation trajectories, from Figure 4. The small green dots in each graph indicate the lowest RMSD values. The top two matrices are for the MD simulations, and the bottom two are for the LBMC simulations. RMSD matrices comparing the similarity of each point of the homology-modeled trajectories with each point of the NMR trajectories for the α/β consensus regions. The RMSD values calculated for the same set of residues used in the alignment were calculated using the measure RMSD function of VMD. maritima, all residues were included except 151. Prior to the RMSD calculation of each pair, the structures were aligned, taking into consideration the backbone atoms of the residues that can be aligned without gap in the protein cheW from E. maritima (right).Ĭomparison of the RMSDs between 20 homology models and 20 NMR structures. To measure structure similarity we measure the RMSD per residue between the selected homology model and the NMR structure of E. Mapping of sequence and structural similarity into the CheW structure.Ī. All values were binned in 1% bins and displayed in the histogram format. The pairwise identity between the sequences i and j was calculated for and. Histogram of the pairwise sequence identities for amongst 1,742 non-redundant CheW sequences.
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