As of today, a new version of the P&D portal (01.2023) is available with two brand new compound sets (and several updated ones), downloads extended with the SQLite database and a new version of our High-quality Chemical Probes set with 729 compounds.
The first new set is a set of 66 compounds extracted from the paper by Jayme L. Dahlin et al., Reference compounds for characterizing cellular injury in high-content cellular morphology assays, published in Nature Communications. As the title suggests, it is "a proposed informer set of control compounds to model cell injury phenotypes in HCS and other phenotypic assays including mechanism-based and nonspecific modes of gross cellular injury". It is interesting that there is almost no overlap between the two sets from the JUMP-Cell painting consortium having only two common compounds with the JUMP-MOA set and two different compounds in common with the JUMP-Target set.
The second new set, from CovBinderInPDB, is a set of 2,183 standardized covalent binders originally extracted from the RSCB Protein Data Bank (PDB) and published in the Journal of Chemical Information and Modeling. "The CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains." As with the first set, it is really interesting that the overlap of this set with another set of covalent binders from CovalentInDB (containing 6,690 compounds) is very low, with only 202 common compounds. To get all covalent binders currently present at the P&D portal, you can easily use the covalent binder tag. Most of them also have directly assigned the target they bind covalently to.
Based on the updated data, our proposed High-quality Chemical Probes (HQCP) set in its latest version contains 729 selected compounds (+15 compared to the 04.2022 version) for 558 primary targets. For a detailed overview of all compounds labelled as chemical probes (both experimental and calculated), you can download extensive probe-focused export in our Download section (here).
As always, you can download all data used on the portal as a PostgreSQL database dump here. and, based on a user request, from P&D ver. 01.2023, you can also download the same data in the SQLite database format (also in the Download section).
We hope you'll find the new data/features useful and if you have any questions or suggestions or if you stumble upon a bug, don't hesitate to contact us through our contact form.