Fig. 1
Distribution of Docking Scores and MM-PBSA Free Energy Values Across Clusters of 102 Chemicals. Negativity indicates higher affinities. (a) Histogram displaying the distribution of docking scores. (b) Histogram illustrating the distribution of MM-PBSA free energy values. (c) Principal Component Analysis (PCA) plot of the first two principal components (PC1 and PC2) using Morgan chemical fingerprints as features, resulting in five distinct clusters, each represented by a different color. (d) Box plot of the docking scores across different clusters. (e) Box plot of single point MM-PBSA free energy. The colors correspond to different clusters, highlighting the variation in docking scores and MM-PBSA values within and between clusters. For comparison, a known high affinity and selected RXR ligand, bexarotene (DTXSID1040619), was included in cluster 4 and has docking and MM-PBSA scores of 16.44 and -87.70, respectively. For, compound that is not known to interact with RXRs, such as tri-iodothyronine (DTXSID8023216), docking failed to generate any binding pose, consistent with its known lack of affinity for RXRs.
