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. Author manuscript; available in PMC: 2018 Jun 13.
Published in final edited form as: J Chem Theory Comput. 2017 May 1;13(6):2930–2944. doi: 10.1021/acs.jctc.6b01183

Figure 7.

Figure 7

Configuration space comparison between YANK and AlGDock. 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 from (a) indole and (b) methanol were projected on the first two principal components. The histograms are plotted on a logarithmic scale. The black dots are projections of the 576 snapshots used in AlGDock calculations onto the same eigenvectors.