ChEMBL Resources

The SARfaris: GPCR, Kinase, ADME

Sunday, 13 November 2011

Recommendations for a MySQL Chemical Data Cartridge?

What options are there for a MySQL Chemical Structure Cartridge ? - the constraints are that the license needs to be Open (to commercial and non-commercial users). Post away in the comments, then everyone can see the answers.

Update: for a little background on our specific interests - we wish to build a deployable and distributable version (a package or vm) with a preconfigured and loaded current ChEMBL database, capable of performing full chemical search capability. Deployment could be as a Linux style package, or as an Amazon EC2 instance. Our internal systems here at the EBI are based on Oracle, and the MDL (or whatever the current name is :) ) Direct cartridge - this configuration is sometimes beyond the reach of many budgets, and so we are interested in exploring a 'free' but useful version of ChEMBL.

Update 2: So Postgres opens up quite a few more options....


Egon Willighagen said...

There is MyChem:

MyChem is developed by Jerome Pansanel, and with OrChem (Mark + Christoph, EBI) part of the ChemiSQL project, that aim at creating a unified API independent of the actual database platform.

Chris said...

Might be worth looking at Bingo

fredrik said...

I believe Bingo doesn't support MySQL, only Oracle, MS SQL, and postgreSQL.

jpo said...

I was mailed about MolCart which is a MySQL chemical data cartridge - more details here

(however, the license looks an issue here, maybe)

greg landrum said...

If you're willing to support postgresql (another popular and powerful open-source database), then another couple options become available: bingo (already mentioned above), and the rdkit (

Both support substructure and similarity searching and are actively maintained.