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Awesome list of computational biology.
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Mar 17, 2024
Machine Learning Tasks and Models / Pre-trained embedding
- Evolutionary Scale Modeling (⭐2.7k) - a library for protein embeddings.
- ChemBERTa-2 (⭐350) - a library for chemical embeddingg and prediction.
Machine Learning Tasks and Models / LLM for biology
- AI4Chem/ChemLLM-7B-Chat - LLM for chemical and molecule science
- BioGPT (⭐4.2k) - LLM for Biomedical text generation
Nov 29, 2023
Databases / Compound
- Drug Repurposing Hub - Collections of drug repurposing data containing drug, moa, target etc.
Databases / Protein
- AlphaFold Protein Structure Database - Database of 3D protein structures.
Databases / Interaction
- Protein-Protein Interaction
Sep 07, 2023
Databases / Compound
- Rhea - Database of chemical reactions.
Jun 13, 2023
Databases / scRNA
- Single Cell Expression Atlas - Public database for single cell RNA.
Databases / Pathway
- PathwayCommons - Database of Pathways and Interactions.
Databases / Genome
- cBioPortal - Database of Cancer Genomics. This has overall metaview for a lot of patients.
Preprocess / Interaction
- Scanpy - scRNA analysis library in Python.
- Seurat - scRNA analysis library in R.
Apr 17, 2023
Databases / scRNA
- Gene Expression Omnibus - Public functional genemics database.
- Single Cell PORTAL - Public database for single cell RNA.
Dec 29, 2022
Databases / Interaction
- Drug (-Cell line) Response
- 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
- 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 (⭐463) - A software of cheminformatics and Machine Learning.
- RDKit (⭐2.4k) - A software of cheminformatics and Machine Learning.
Machine Learning Tasks and Models / Drug Repurposing
- DeepPurpose (⭐878) - A DL Library for Drug Repurposing and so on.
Machine Learning Tasks and Models / Drug Target Interaction
- NeoDTI (⭐71) - 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 (⭐126) - 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.
- Comparative Toxicogenomics Database - A database for drug-target interactions.
- Therapeutics Data Commons - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.
- Chemical Protein Interaction
Machine Learning Tasks and Models / Drug Repurposing
- DRKG (⭐537) - A library for biological knowledge graph.