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Configuration space comparison between YANK samples from (a) all active and (b) all inactive ligands. Principal components analysis was performed on snapshots from all YANK simulations for heavy atoms within 5 Å of Val 111 in PDB ID 3DMZ. Two-dimensional histograms, weighted by Eq. 5, of YANK snapshots were projected on the first two principal components. The histograms are plotted on a logarithmic scale.
