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 […]

Computational Research and Software in Academia

This paper by Prof. Tim Pederson in the Journal of Computational Linguistics highlights the need for authors of computational linguistics papers to release working software that can be used to reproduce results in their papers. While the paper focuses on the field of computational linguistics (CL), the discussion is perfectly applicable to other fields that […]