Datasets for Virtual Screening Benchmarks

Virtual screening (VS) is a common task in the drug discovery process and is a computational method to identify¬† promising compounds from a collection of hundreds to millions of possible compounds. What “promising” exactly means, depends on the context – it might be compounds that will likely exhibit certain pharmacological effects. Or compounds that are […]

Which Bits are Important for Similarity Searches?

The recent paper by Wang and Bajorath is an interesting approach to identifying the important bits in a fingerprint, with respect to a dataset. Their discussion focuses on the structural key type fingerprints (such as MACCS and the BCI fingerprints) and the problem they are trying to address is the fact that certain structural features […]

AJAX’ified Pub3D

Pub3D is a 3D version of PubChem, in which we have generated a single conformer for 99% of PubChem using the smi23d suite of programs. The structures are then stored in a PostgreSQL database along with their distance moment shape descriptors described by Ballester and Graham-Richards. This allows us to perform shape similarity queries against […]