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data

Source data

The CC capitalizes on many data sources. The following is an extensive list of resources that are worth considering in current and future versions of the CC. Inside each CC level, I list the resources in alphabetical order. Please feel free to update the list at any time.

I recommend visiting the NAR Online Molecular Biology Database Collection and OmicsTools to stay up-to-date with data releases. Also, the LINCS Data Portal is of interest.

  • Already in the CC.
  • Not yet in the CC.

Observational data resources

A Chemistry

  • ChemoPy [paper code]
  • A small chemoinformatics library focused on physicochemical properties and some fingerprints.
  • ClassyFire [paper code]
  • Automatic classification of chemical compounds
  • Ontology / taxonomy
  • DeepChem [web code]
  • A powerful deep learning chemoinformatics library, containing a large number of featurizers.
  • Among the interesting featurizers, there are the PDB-crystal embeddings, which should, in principle, enable connectivity between crystals and small molecules.
  • E3FP [paper code]
  • Simple representations of 3D molecular structure.
  • Integrated tightly with RDKIT.
  • molBLOCKS [paper code]
  • Decompose small molecules into fragments (scaffolds).
  • PyBioMed [paper code]
  • A number of physicochemical descriptors and the common fingerprints. Very similar to ChemoPy.
  • It can also featurize sequence data (protein and DNA).
  • RDKIT [paper code]
  • The standard library for chemoinformatics in python.
  • Calculates several fingerprints and also does 3D conformational sampling.
  • Silicos-IT [web code]
  • It has implementations for the chemical beauty score (QED).

B Targets

  • BindingDB [paper data]
  • Chemical-protein binding data (patents)
  • ChEMBL [paper data]
  • Known drug targets
  • Drug metabolizing enzymes
  • Chemical-protein binding
  • Chemical-target-based assay activity
  • Comparative Toxicogenomics Database (CTD) [paper data]
  • Chemical-gene interaction data, including regulatory interactions
  • Drug Repositioning Hub [paper data]
  • Drug indications
  • DrugBank [paper data]
  • Known drug targets with pharmacological action
  • Drug metabolizing enzymes
  • Drug (off-)targets
  • Human Metabolome Database [paper data]
  • Metabolizing enzymes
  • LINCS touchstone targets [paper data]
  • Well annotated targets of a reference set of molecules
  • PubChem Bioassays [paper data]
  • Repository of bioassay data
  • It contains softly-annotated targets
  • STITCH [paper data]
  • Integrative compound-protein interaction database
  • It has orthology mapping
  • Therapeutic Target Database [paper data]
  • Mode of action of drugs
  • Vogt et al. Future Science OA (2018) [paper]
  • Computationally derived compound profiling matrices

C Networks

  • Chemical Entities of Biological Interest (ChEBI) [paper data]
  • Chemical ontology of biological roles
  • InWEB [paper data]
  • Integrative protein interaction database
  • Kyoto Encyclopedia of Genes and Genomes (KEGG) [paper data]
  • A standard pathway database
  • MetaPhORS [paper data]
  • Orthology and paralogy relationships between genes
  • PathwayCommons [paper data]
  • Integrative interaction database, using pathway data
  • Reactome [paper data]
  • A standard pathway database
  • Recon [paper data]
  • Currently, we are using version 1 of Recon.
  • STRING [paper data]
  • Protein interaction database
  • Includes physical and regulatory interactions

D Cells

  • Broad Therapeutics morphology data [paper data]
  • 812-feature cell-painting assays
  • Cancer Therapeutic Response Portal (CTRP) [paper data]
  • Large cell line panel of drug sensitivity profiles.
  • ChEMBL [paper data]
  • Literature cell-based assays
  • Clue.io morphology [data]
  • Cell painting assay
  • Genomics of Cell Sensitivity in Cancer (GDSC) [paper data]
  • Large cell line panel of drug sensitivity profiles
  • MOSAIC [paper data]
  • Chemical-genetic interaction data in yeast
  • Next-Generation L1000 Connectivity Map [paper data]
  • Transcriptomics perturbational data
  • NCI-60 [paper data]
  • Cell-line growth-inhibition data

E Clinics

  • ChEMBL [paper data]
  • Drug indications
  • Therapeutic areas
  • Comparative Toxicogenomics Database (CTD) [paper data]
  • Compound-disease associations
  • Drug Repositioning Hub [paper data]
  • Drug indications
  • DrugBank [paper data]
  • Drug-drug interactions
  • Therapeutic areas
  • DrugCentral [paper data]
  • Drug indications
  • Drug side effects
  • Kyoto Encyclopedia of Genes and Genomes (KEGG) [paper data]
  • Therapeutic areas
  • OFFSIDES [paper data]
  • Side effects
  • Side Effect Resource (SIDER) [paper data]
  • Drug side effects
  • RepoDB [paper data]
  • Drug indications
  • TWOSIDES [paper data]
  • Drug-drug interactions

Prediction and calculation methods

⚠ This section is largely incomplete because we haven't explored it properly, yet.

  • PIDGIN [paper code]
  • Target prediction trained with negative data.