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ChemicalToolBoX Cheminformatics inside the Galaxy

October 2012 • Björn Grüning

"Enable accessible, reproducible, and transparent computational research."
"Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery."

Wikipedia

- paint your structure

- upload molecule files

- download pubchem

SMILES: CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O
InChI-Key: BQJCRHHNABKAKU-KBQPJGBKSA-N

molecule datatypes are first class citizen

- SMILES

- InChI

- MOL/SDF

- MOL2

- CML

fingerprint generation

- Daylight Fingerprint

- PubChem Finperprint

- MACCS

- ...

| large scale postgresql :: pgchem

filtering

- predefined rules (drug-like, lead-like, lipinski-conform ...)

- physicochemical properties

- Similarity Search

- Substructure Search

- Pharmacophore Search

- Spectrophore Search

the big picture

- 32 different tools

- powered by open source projects

- offer a community starting point

some use cases from our lab

- building comprehensive and specialised compound libraries

- screening libraries for new drug candidates

- exploring of the chemical universe

ChemicalBoX
"... is a comprehensive collection of small compounds, consisting of data from other repositories. The focus of ChemicalBoX is to offer a ready- and easy-to-use compound library that extends current freely available compilations."

- reproducibility/transparency

- completeness

- free availability

- automatization

- 39 million filtered unique compounds

ftp://pharmaceutical-bioinformatics.org/chemicalbox/

git clone http://chemicalbox.pharmaceutical-bioinformatics.org/chemicalbox.git

PurchasableBoX
"... is a comprehensive collection of small compounds,
consisting of data from various vendors."

- 44,6 million filtered unique compounds

- 43,6 million drug like compounds (qed > 0.2)

- 1,2 million cluster centers (similarity > 0.85)

Merging ChemicalBoX and PurchasableBoX offers a compilation
of ~65 million of unique filtered compounds.
Merging ChemicalBoX and PurchasableBoX offers a compilation
of ~65 million of unique filtered compounds.
Exploring new areas of the chemical universe.

- fragmentation of 1.425 drugs

- 1.895 fragments

- 182.360 unique, merged compounds

- 150.642 are druglike (qed > 0,3)

G. Richard Bickerton et al. "Quantifying the chemical beauty of drugs"; Nature Chemistry 2012

### Questions?

Thank You!

Björn Grüning

bjoern.gruening@gmail.com

www.pharmaceutical-bioinformatics.org

https://github.com/bgruening https://bitbucket.org/BjoernGruening