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Awesome list of computational biology.

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[ Daily / Weekly / Overview ]

Dec 29, 2022

Databases / Genome

• NCI60 A database which focus on 60 cancer cell lines with many drugs.

• Genomics of Drug Sensitivity in Cancer (GDSC) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.

• Cancer Cell Line Encyclopedia - A database of cancer cell lines. This has 1000 cell lines.

May 18, 2022

Databases / Compound

• ChEBI - Chemical database focused on small chemical compounds.

Databases / Protein

• PROTEIN DATA BANK - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.

May 15, 2022

Databases / Compound

• PubChem - One of the biggest chemical database such as compounds, genes and proteins.

• ChEMBL - Database of bioactive molecules with drug-like properties.

• ChemSpider - Chemical structure database.

• KEGG COMPOUND - Collection of small molecules and biopolymers.

• LIPID MAPS - Database of lipids.

Databases / Pathway

• PathwayCommon - Database of Pathways and Interactions.

• KEGG PATHWAY - Collection fo drawn pathway maps.

• WikiPathways - Database of biological pathways.

Databases / Mass Spectra

• MassBank - Open souce databases and tools for mass spectrometry reference spectra.

• MoNA MassBank of North America - Meta database of metabolite mass spectra, metadata and associated compounds.

Databases / Protein

• THE HUMAN PROTEIN ATLAS - One of the biggest human protein database contained cells, tissues, and organs.

• UniProt - The collection of functional information on proteins.

Databases / Genome

• Human Genome Resources at NCBI - Database of image, proteomics, transcriptomics and systems biology.

• GenBank - Database of genetic sequence offered by NCBI.

• UCSC Genome Browser - Genome blowser offered by UCSC.

Databases / Disease

• KEGG DRUG - Comprehensive drug information resource for approved drugs.

Preprocess / Interaction

• Chemistry Development Kit (⭐387) - A software of cheminformatics and Machine Learning.

• RDKit (⭐1.9k) - A software of cheminformatics and Machine Learning.

Machine Learning Tasks and Models / Drug Repurposing

• DeepPurpose (⭐683) - A DL Library for Drug Repurposing and so on.

Machine Learning Tasks and Models / Drug Target Interaction

• NeoDTI (⭐62) - A library for Drug Target Interaction.

Machine Learning Tasks and Models / Compound Protein Interaction

• MCPINN (⭐3) - A library for drug discovery using Compound Protein Interaction and Machine Learning.

• TransformerCPI (⭐84) - A library for Compound Protein Interaction prediction using Transformer.

Feb 22, 2022

Databases / Disease

• DrugBank - A database of drug and target maintained by the University of Alberta.

Databases / Interaction

• Drug Gene Interaction
  • DGIdb - A database of drug-gene interactions and the druggable genome.
  • Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
  • SNAP - A dataset which contains Drug-gene interactions.

• Chemical Protein Interaction
  • STITCH - A database of Chemical Protein Interaction.

Machine Learning Tasks and Models / Drug Repurposing

• DRKG (⭐452) - A library for biological knowledge graph.