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Figure 5.16 (A) COST versus rank for the NOE matching run on Bcl-x L / 7 poses using the
protein coordinates from 1MAZ. The poses of the NOE matching run are ordered based on
COST and plotted from lowest COST to highest COST. (B) Superposition of target pose and the
minimum cost pose (dark gray) from (A). The side-chains of F97, Y101 and R139 from 1YSG
(thin light gray) and 1MAZ (thin dark gray) are also displayed.
the code for dealingwith larger numbers of poses, 10 000 poses were selected from the Poser
ensemble based on an RMSD sampling for evaluation with NOE matching. NOE matching
was applied using our 57 experimental intermolecular NOEs and with the predicted protein
resonance assignments set to the corresponding BMRB average values. The COST values
from NOE matching ranged from 1246 to 5023 (Figure 5.17A). Clustering of the poses
based on RMSD and a similarity of 0.8 Ă… resulted in 1222 clusters, of which 260 were
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Figure 5.17 (A) COST versus rank for the NOE matching run on Bcl-x L / 7 poses using the
protein coordinates from 1BXL. The poses of the NOE matching run are ordered based on
COST and plotted from lowest COST to highest COST. (B) Superposition of target pose and the
minimum cost pose (dark gray) from (A). The side-chains of F97, Y101 and R139 from 1YSG
(thin light gray) and 1BXL (thin dark gray) are also displayed.
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