In drug discovery and drug development, docking-based virtual screening and pharmacophore-based virtual screening assist the hit discovery and lead optimization in a fast and cost-efficient way. These methods represent a key tool in the field, which enables to computationally screen large libraries of compounds. However, the selection of appropriate candidates as well as dealing with false-positive still represents a challenge in the post-screening evaluation. In this context, Cluph is a chemoinformatic tool built for the intended purpose of finding hits compounds that come from virtual screening, both pharmacophore-based and docking-based.
To use Cluph, molecular descriptor for each chemical entity should be generated (PaDEL can be used for this purpose). Then, Principal Component Analysis (PCA) is performed to reduce the dimension of the data by eliminating the least significant molecular descriptors. Finally, compounds are clusterized using Hierarchical Clustering method.
Cluph detects the number of components to keep by identifying the inflection point. At this step, it will ask the user to input the number of principal components to be retained. On the selected PCs, Hierarchical clustering is performed and a dendrogram will appear. Again, based on the dendrogram, Cluph will ask the user to tell him how many clusters were generated