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. Some resources may be repeated because some of them have different types of data.

I recommend visiting the NAR Online Molecular Biology Database Collection and OmicsTools to stay up-to-date with the literature.

• 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
• 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
• 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

• Genomics of Cell Sensitivity in Cancer (GDSC)
• Cancer Cell Line Enciclopedia (CCLE)
• NCI-60
• CTRP
• [ ]

E Clinics

• [X]

Prediction tools