Cluster compounds visualization

The final library was designed with the purpose of adding incremental diversity to the first three fragment libraries. The main filtering criterion was novel pharmacophoric triangles not found in the first three libraries. After clustering and visual inspection from a panel of medicinal chemists, only 65 compounds were purchased and 61 compounds passed QC. 

A significant percentage of any compound library will inevitably fall into small clusters unsuitable to rigorous statistical evaluation. These must be considered separately - in our case, using diversity analysis with BCUT descriptors [39] to supplement the list derived from clustering. Throughout this process, we use visualization to assess data quality, identify potential problems such as edge effects, and check trends and patterns. 

Key Words Biological activity chemical features chemical space cluster analysis compound databases dimension reduction molecular descriptors molecule classification partitioning algorithms partitioning in low-dimensional spaces principal component analysis visualization. 

Cluster 5 Nutmeg and MDA, the empathic compounds that create few "visuals, stimulating research into discrete psychedelic effects... 

The seven compounds were first subjected to an exhaustive conformational search utilizing the Monte Carlo (MC) Multiple Minimum algorithm as available in MacroModel. The resulting conformers were then clustered using distances between the potential pharmacophore features. A minimum energy conformation in each of the clusters was used as input to DISCO algorithm. DISCO models were visually inspected and one of them was used as a 3-D query in the... 

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