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Awesome list of computational biology.

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[ Daily / Weekly / Overview ]

Feb 08, 2026

Pathway

• Reactome — Expert-curated, peer-reviewed pathway database with detailed reaction mechanisms.

• BioCyc — Collection of pathway/genome databases across thousands of organisms.

• SIGNOR — Database of causal signaling interactions and pathways.

• MSigDB (Molecular Signatures Database) — Curated gene sets derived from pathways and biological processes.

Protein

• PROTEIN DATA BANK (PDB) — 3D structures of proteins, nucleic acids, complexes.

• RCSB Protein Data Bank — Repository for structural data of biological molecules.

Disease

• DrugBank — Database of drugs and targets (University of Alberta).

Interaction / Drug-Gene Interaction

• Comparative Toxicogenomics Database — Chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype associations.

• SNAP — Dataset of drug-gene interactions.

• Therapeutics Data Commons — Datasets for drug-target, response, drug-drug interaction, etc.

Interaction / Drug (Cell Line) Response

• Genomics of Drug Sensitivity in Cancer (GDSC) — Drug sensitivity for ~1000 human cancer cell lines and hundreds of compounds.

• Cancer Cell Line Encyclopedia — Database of ~1000 cancer cell lines.

• CellMiner Cross Database (CellMinerCDB) — Integrates multiple cancer cell line databases.

Interaction / Chemical-Protein Interaction

• BindingDB — Compounds and target database.

• PDBBind — Binding affinity data for biomolecular complexes.

• CrossDocked2020 — Large-scale dataset for structure-based virtual screening.

Interaction / Protein-Protein Interaction

• BioGRID — Protein, genetic, and chemical interactions.

• HIPPIE — Human protein-protein interaction database.

Interaction / Knowledge Graph

• DRKG (⭐670) — Large-scale biological knowledge graph for drug discovery.

• Hetionet (⭐340) — Heterogeneous network integrating genes, diseases, drugs, pathways, and more.

• OpenBioLink (⭐157) — Benchmark datasets for biological knowledge graph completion.

• PrimeKG (⭐697) — Multi-modal precision medicine knowledge graph integrating clinical, genetic, and drug data.

API / Knowledge Graph

• PubMed E-utilities (esearch/efetch) — APIs for searching and retrieving biomedical literature from PubMed.

• NCBI E-utilities — Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc).

• UniProt REST API — Programmatic access to protein sequence and functional annotation data.

• Ensembl REST API — API for genomic annotations, variants, genes, and comparative genomics.

• KEGG REST API — API for accessing KEGG pathways, compounds, genes, and reactions.

• ChEMBL Web Services — REST API for bioactive molecules, targets, and bioassays.

• Open Targets Platform API — API for target–disease associations integrating genetics, genomics, and drug data.

• ClinicalTrials.gov API — API for querying clinical trial metadata and results.

Drug Target Interaction / Knowledge Graph

• DTINet (⭐185) — Network-based framework integrating heterogeneous biological data for DTI prediction.

• DeepDTA (⭐291) — Deep learning model using CNNs on protein sequences and drug SMILES.

• GraphDTA (⭐292) — Graph neural network–based DTI prediction using molecular graphs.

• MolTrans (⭐224) — Transformer-based DTI model leveraging molecular substructures.

• DrugBAN (⭐140) — Bilinear attention network for interpretable DTI prediction.

Pre-trained Embedding / Knowledge Graph

• Evolutionary Scale Modeling (ESM) (⭐4k) — Protein embeddings.

Jan 07, 2026

Preprocessing Tools / Knowledge Graph

• ChatSpatial (⭐11) — MCP server for spatial transcriptomics analysis via natural language.

Foundation Models / Knowledge Graph

• scFoundation (⭐390) — Large-scale foundation model for single-cell gene expression, enabling multiple downstream tasks.

• scGPT (⭐1.5k) — Transformer-based foundation model pretrained on millions of single-cell profiles.

• BulkFormer (⭐41) — Foundation model for bulk RNA-seq data; learns general transcriptomic representations.

Jan 03, 2026

Preprocessing Tools / Knowledge Graph

• FlashDeconv (⭐10) — High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min).

• Squidpy — Python library for spatial single-cell analysis.

Nov 17, 2024

Drug Response Prediction / Knowledge Graph

• MOFGCN (⭐6) — GCN + heterogeneous network.

• DeepDSC — Autoencoder + fully connected NN.

• DGDRP (⭐0) — Multi-view embedding neural network.

• DeepAEG (⭐3) — GNN embedding + attention mechanism.

Sep 01, 2024

Compound

• ZINC ligand discovery database — Free database of commercially-available compounds for virtual screening.

• MoleculeNet — Benchmark datasets for molecular machine learning.

Protein

• Critical Assessment of Structure Prediction (CASP) — Assessing methods for protein structure prediction.

• Uniclust — Clustered protein sequence databases.

• CATH database — Hierarchical classification of protein domain structures.

Genome

• 10x Genomics Dataset — Collection of single-cell datasets.

• The Genotype-Tissue Expression (GTEx) — Human gene expression and regulation resource.

• Dependency Map (DepMap) — CRISPR-Cas9 screens in cancer cell lines.

• Catalogue Of Somatic Mutations In Cancer (COSMIC) — Resource on somatic mutations in cancers.

• MGnify — Resource for metagenomic and metatranscriptomic data.

• JASPAR — Database of transcription factor binding profiles.

Clinical Trial / Knowledge Graph

• ClinicalTrials.gov — Privately and publicly funded clinical studies.

• ICD10 — International Classification of Diseases, 10th revision.

• EU Drug Regulating Authorities Clinical Trials DB (EudraCT) — European clinical trial database.

• MIMIC-IV — Freely accessible critical care database.

Aug 11, 2024

Compound

• Therapeutic Target Database — Drug-target, target-disease, and drug-disease datasets.

Aug 10, 2024

LLM for Biology / Knowledge Graph

• scPRINT (⭐138) — Pretrained on 50M cells for scRNA-seq denoising & zero imputation.

Jul 17, 2024

Interaction / Knowledge Graph

• Drug Mechanism Database (DrugMechDB) (⭐67) — Mechanisms of action from drug to disease.

Drug Response Prediction / Knowledge Graph

• drGAT (⭐1) — Attention-based model for drug response prediction with gene explainability.

LLM for Biology / Knowledge Graph

• GeneGPT (⭐420) — LLM for biomedical information, integrated with various APIs.

• GenePT (⭐308) — Foundation LLM for single-cell data.

Mar 17, 2024

Pre-trained Embedding / Knowledge Graph

• ChemBERTa-2 (⭐486) — Chemical embeddings & prediction.

LLM for Biology / Knowledge Graph

• AI4Chem/ChemLLM-7B-Chat — LLM for chemical & molecular science.

• BioGPT (⭐4.5k) — LLM for biomedical text generation.

Nov 29, 2023

Compound

• Drug Repurposing Hub — Collections of drug repurposing data (drug, MoA, target, etc).

Protein

• AlphaFold Protein Structure Database — 3D protein structure predictions.

Interaction / Protein-Protein Interaction

• STRING — PPI networks for multiple organisms.

Sep 07, 2023

Compound

• Rhea — Database of chemical reactions.

Jun 13, 2023

scRNA

• Single Cell Expression Atlas — Public database for single-cell RNA.

Pathway

• PathwayCommons — Database of pathways and interactions.

Genome

• cBioPortal — Cancer genomics database; aggregating many patient datasets.

Preprocessing Tools / Knowledge Graph

• Scanpy — Python library for scRNA-seq analysis.

• Seurat — R library for scRNA-seq analysis.

Apr 17, 2023

scRNA

• Gene Expression Omnibus — Public functional genomics database.

• Single Cell PORTAL — Public database for single-cell RNA.

Dec 29, 2022

Interaction / Drug (Cell Line) Response

• NCI60 — Focuses on 60 cancer cell lines and many drugs.

May 18, 2022

Compound

• ChEBI — Database focused on small chemical compounds.

May 15, 2022

Compound

• PubChem — One of the largest chemical databases (compounds, genes, and proteins).

• ChEMBL — Bioactive molecules with drug-like properties.

• ChemSpider — Chemical structure database.

• KEGG COMPOUND — Collection of small molecules and biopolymers.

• LIPID MAPS — Database of lipids.

Pathway

• KEGG PATHWAY — Collection of pathway maps.

• WikiPathways — Database of biological pathways.

Mass Spectra

• MassBank — Open source databases and tools for mass spectrometry reference spectra.

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

Protein

• THE HUMAN PROTEIN ATLAS — Comprehensive human protein database (cells, tissues, organs).

• UniProt — Functional information on proteins.

Genome

• Human Genome Resources at NCBI — Database for genomics, proteomics, transcriptomics, and systems biology.

• GenBank — NCBI's database of genetic sequences.

• UCSC Genome Browser — UCSC's genome browser.

Disease

• KEGG DRUG — Comprehensive, approved drug information.

Preprocessing Tools / Knowledge Graph

• Chemistry Development Kit (⭐568) — Cheminformatics software & machine learning tools.

• RDKit (⭐3.3k) — Cheminformatics software & machine learning toolkit.

Drug Repurposing / Knowledge Graph

• DeepPurpose (⭐1.1k) — Deep learning library for drug repurposing.

Drug Target Interaction / Knowledge Graph

• NeoDTI (⭐77) — Library for drug-target interaction prediction.

Compound-Protein Interaction / Knowledge Graph

• MCPINN (⭐3) — Drug discovery via compound-protein interaction and machine learning.

• TransformerCPI (⭐152) — CPI prediction using Transformer.

Feb 22, 2022

Interaction / Drug-Gene Interaction

• DGIdb — Drug-gene interactions and the druggable genome.

Interaction / Chemical-Protein Interaction

• STITCH — Chemical-protein interactions.