Exploration of Chemical Datasets using UMAP. Detailed analysis of how UMAP embeds a MoleculeNet dataset and practical uses for UMAP at Reverie Labs.
In this post, we’ll discuss how we manage and process PDBs, a critical chemical data filetype that encodes the 3-D structure of proteins. What is a PDB? At Reverie, we use 3D protein structural data for many applications - medicinal chemists evaluating structure-activity relationships, computational chemists running molecular dynamics
A quick-and-dirty way to clean noisy datasets before training on them