Clustering of Small Molecules Based on Similarity Scores From Flexible 3D Alignment

There are several approaches for clustering chemical structures. Among these, the structure-based methods and techniques using classical 2D descriptors (e.g. chemical fingerprints or ECFP) are the most widely used. Considering 3D information, such as conformers, 3D pharmacophore maps or molecular shapes can provide researchers more insight into the process and facilitate a deeper and more natural interpretability of corresponding results. ChemAxon’s 3D alignment tool provides an automatic 3D shape-based flexible alignment option for handling small molecules and the resulting shape similarity scores calculated for the best fits can be further used in similarity-based clustering as a part of scaffold hopping for finding new lead molecules.

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