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Awesome list of computational biology.
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Jan 02, 2026
Preprocess / Clinical Trial
- FlashDeconv (⭐3) - High-performance spatial transcriptomics deconvolution. Processes 1M spots in ~3 minutes.
- Squidpy - Spatial single cell analysis library in Python.
Nov 17, 2024
Drug Response Prediction / Clinical Trial
- MOFGCN (⭐6): GCN + heterogeneous network
- DeepDSC: Autoencoder + Fully Connected NN
- DGDRP (⭐0): Multi-view embedding NN.
- DeepAEG (⭐3): GNN Embedding + Attention
Aug 31, 2024
Databases / Compound
- ZINC ligand discovery database - Free database of commercially-available compounds for virtual screening.
- MoleculeNet - Benchmark for molecular machine learning.
- Ames Mutagenicity dataset - Dataset for predicting mutagenicity.
- ADCdb - Database for antibody-drug conjugates.
Databases / Protein
- RCSB Protein Data Bank (PDB) - Repository of 3D structural data of large biological molecules.
- Critical Assessment of Structure Prediction (CASP) - Experiment for advancing the methods of predicting protein structure from sequence.
- Uniclust - Collection of clustered protein sequence databases.
- CATH database - Hierarchical classification of protein domain structures.
Databases / Genome
- 10x Genomics Dataset - Collection of single-cell datasets.
- The Genotype-Tissue Expression (GTEx) - Resource for studying human gene expression and regulation.
- Dependency Map (DepMap) - Genome-wide CRISPR-Cas9 screens in cancer cell lines.
- Catalogue Of Somatic Mutations In Cancer (COSMIC) - Comprehensive resource for exploring somatic mutations in human cancers.
- MGnify - Free resource for archiving, analysis, and browsing of metagenomic and metatranscriptomic data.
- JASPAR - Open-access database of curated, non-redundant transcription factor binding profiles.
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.
- CellMiner Cross Database (CellMinerCDB) - Integration of multiple cancer cell line databases.
- Chemical Protein Interaction
- STITCH - A database of Chemical Protein Interaction.
- BindingDB - A database of compounds and targes.
- PDBBind - Database of experimentally measured binding affinity data for biomolecular complexes.
- CrossDocked2020 - Large-scale dataset for machine learning in structure-based virtual screening.
Databases / Clinical Trial
- ClinicalTrials.gov - Database of privately and publicly funded clinical studies.
- ICD10 - International Classification of Diseases, 10th revision.
- EU Drug Regulating Authorities Clinical Trials DB (EudraCT) - European database of clinical trials.
- MIMIC-IV - Freely accessible critical care database.
Aug 10, 2024
Databases / Compound
- Therapeutic Target Database - collections of drug-target, target-disease, and drug-disease dataset.
Databases / Interaction
- Knowledge Graph
- Drug Mechanism Database (DrugMechDB) (⭐65): database of the mechanism of action from a drug to a disease.
- DRKG (⭐664) - A library for biological knowledge graph.
Drug Response Prediction / Drug Repurposing
- DeepPurpose (⭐1.1k) - A DL Library for Drug Repurposing.
Aug 09, 2024
Drug Response Prediction / LLM for biology
- scPRINT (⭐127) - scPRINT is pretrained on 50M cells to denoise and perform zero imputation of any single cell RNAseq profile.
Jul 16, 2024
API / Clinical Trial
- PubMed esearch: API for searching articles in PubMed.
Drug Response Prediction / Clinical Trial
- drGAT (⭐1): A model for drug response prediction with gene explainability with attention mechanism.
Drug Response Prediction / LLM for biology
- GeneGPT (⭐418) - LLM for biomedical information with several API.
- GenePT (⭐299) - foundation LLM for single cell data
Mar 16, 2024
Drug Response Prediction / Compound Protein Interaction
- TransformerCPI (⭐151) - A library for Compound Protein Interaction prediction using Transformer.
Drug Response Prediction / Pre-trained embedding
- Evolutionary Scale Modeling (⭐3.9k) - a library for protein embeddings.
- ChemBERTa-2 (⭐477) - a library for chemical embeddingg and prediction.
Drug Response Prediction / LLM for biology
- AI4Chem/ChemLLM-7B-Chat - LLM for chemical and molecule science
- BioGPT (⭐4.5k) - LLM for Biomedical text generation
Nov 28, 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.
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.
- Therapeutics Data Commons - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.
Preprocess / Clinical Trial
- Scanpy - scRNA analysis library in Python.
- Seurat - scRNA analysis library in R.
Apr 16, 2023
Databases / scRNA
- Gene Expression Omnibus - Public functional genemics database.
- Single Cell PORTAL - Public database for single cell RNA.
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 / Clinical Trial
- Chemistry Development Kit (⭐559) - A software of cheminformatics and Machine Learning.
- RDKit (⭐3.2k) - A software of cheminformatics and Machine Learning.
Drug Response Prediction / Drug Target Interaction
- NeoDTI (⭐77) - A library for Drug Target Interaction.
Drug Response Prediction / Compound Protein Interaction
- MCPINN (⭐3) - A library for drug discovery using Compound Protein Interaction and Machine Learning.
Feb 22, 2022
Databases / Disease
- DrugBank - A database of drug and target maintained by the University of Alberta.