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Awesome list of computational biology.
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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.