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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.


transparent
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