{"id":637,"url":"https://github.com/inoue0426/awesome-computational-biology","last_synced_at":"2025-08-13T20:32:07.565Z","repository":{"id":41888503,"uuid":"459787963","full_name":"inoue0426/awesome-computational-biology","owner":"inoue0426","description":"Awesome list of computational biology.","archived":false,"fork":false,"pushed_at":"2024-11-17T03:42:01.000Z","size":117,"stargazers_count":97,"open_issues_count":0,"forks_count":5,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-08-10T14:15:14.376Z","etag":null,"topics":["awesome","awesome-list","computational-biology","drug-discovery","drug-repurposing","machine-learning"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/inoue0426.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"contributing.md","funding":null,"license":"LICENSE","code_of_conduct":"code-of-conduct.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2022-02-15T23:46:16.000Z","updated_at":"2025-07-30T20:28:33.000Z","dependencies_parsed_at":"2023-11-29T00:24:01.097Z","dependency_job_id":"bad7919f-3d0c-4009-a97d-2d2944835ece","html_url":"https://github.com/inoue0426/awesome-computational-biology","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/inoue0426/awesome-computational-biology","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inoue0426%2Fawesome-computational-biology","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inoue0426%2Fawesome-computational-biology/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inoue0426%2Fawesome-computational-biology/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inoue0426%2Fawesome-computational-biology/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/inoue0426","download_url":"https://codeload.github.com/inoue0426/awesome-computational-biology/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inoue0426%2Fawesome-computational-biology/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270305842,"owners_count":24562109,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-13T02:00:09.904Z","response_time":66,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["awesome","awesome-list","computational-biology","drug-discovery","drug-repurposing","machine-learning"],"created_at":"2024-01-05T20:13:00.772Z","updated_at":"2025-08-13T20:32:07.273Z","avatar_url":"https://github.com/inoue0426.png","language":null,"funding_links":[],"categories":["Science","Miscellaneous","Uncategorized","Others","Related Resources","Other Lists","Related Awesome Lists","Themed Directories"],"sub_categories":["Uncategorized","\u003ccode\u003eRelated Repositories\u003c/code\u003e","TeX Lists","Tutorials","Subscription Journals","Updated this month","Synthetic DNA \u0026 Gene Synthesis"],"readme":"# Awesome Computational Biology [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)\n\nA knowledge collection of databases, software and papers related to computational biology.\n\n\u003e Computational biology involves the development and application of data-analytical and theoretical methods,\n\u003e mathematical modelling and computational simulation techniques to the study of biological, ecological,\n\u003e behavioural, and social systems. - [Wikipedia](https://en.wikipedia.org/wiki/Computational_biology)\n\n## Contents\n\n- [Databases](#databases)\n  - [scRNA](#scrna)\n  - [Compound](#compound)\n  - [Pathway](#pathway)\n  - [Mass Spectra](#mass-spectra)\n  - [Protein](#protein)\n  - [Genome](#genome)\n  - [Disease](#disease)\n  - [Interaction](#interaction)\n  - [Clinical Trial](#clinical-trial)\n- [API](#api)\n- [Preprocess](#preprocess)\n- [Machine Learning Tasks and Models](#machine-learning-tasks-and-models)\n  - [Drug Response Prediction](#drug-response-prediction)\n  - [Drug Repurposing](#drug-repurposing)\n  - [Drug Target Interaction](#drug-target-interaction)\n  - [Compound Protein Interaction](#compound-protein-interaction)\n  - [Pre-trained embedding](#pre-trained-embedding)\n  - [LLM for biology](#llm-for-biology)\n\n## Databases\n### scRNA\n- [Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/) - Public functional genemics database.\n- [Single Cell PORTAL](https://singlecell.broadinstitute.org/single_cell) - Public database for single cell RNA.\n- [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home) - Public database for single cell RNA.\n### Compound\n- [PubChem](https://pubchem.ncbi.nlm.nih.gov/) - One of the biggest chemical database such as compounds, genes and proteins.\n- [ChEBI](https://www.ebi.ac.uk/chebi/) - Chemical database  focused on small chemical compounds.\n- [ChEMBL](https://www.ebi.ac.uk/chembl/) - Database of bioactive molecules with drug-like properties.\n- [ChemSpider](http://www.chemspider.com/) - Chemical structure database.\n- [KEGG COMPOUND](https://www.genome.jp/kegg/compound/) - Collection of small molecules and biopolymers.\n- [LIPID MAPS](https://www.lipidmaps.org/databases/lmsd/overview) - Database of lipids.\n- [Rhea](https://www.rhea-db.org/) - Database of chemical reactions.\n- [Drug Repurposing Hub](https://repo-hub.broadinstitute.org/repurposing#download-data) - Collections of drug repurposing data containing drug, moa, target etc.\n- [Therapeutic Target Database](https://idrblab.net/ttd/full-data-download) - collections of drug-target, target-disease, and drug-disease dataset.\n- [ZINC ligand discovery database](https://zinc.docking.org/) - Free database of commercially-available compounds for virtual screening.\n- [MoleculeNet](http://moleculenet.ai/) - Benchmark for molecular machine learning.\n- [Ames Mutagenicity dataset](https://www.sciencedirect.com/science/article/abs/pii/S0166354220302412) - Dataset for predicting mutagenicity.\n- [ADCdb](https://www.antibody-drug.com/) - Database for antibody-drug conjugates.\n### Pathway\n- [PathwayCommons](https://www.pathwaycommons.org/) - Database of Pathways and Interactions.\n- [KEGG PATHWAY](https://www.genome.jp/kegg/pathway.html) - Collection fo drawn pathway maps.\n- [WikiPathways](https://wikipathways.org/) - Database of biological pathways.\n### Mass Spectra\n- [MassBank](http://www.massbank.jp/) - Open souce databases and tools for mass spectrometry reference spectra.\n- [MoNA MassBank of North America](https://mona.fiehnlab.ucdavis.edu/) - Meta database of metabolite mass spectra, metadata and associated compounds.\n### Protein\n- [THE HUMAN PROTEIN ATLAS](https://www.proteinatlas.org/) - One of the biggest human protein database contained cells, tissues, and organs. \n- [PROTEIN DATA BANK](https://www.rcsb.org/) - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.\n- [UniProt](https://www.uniprot.org/) - The collection of functional information on proteins.\n- [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/api-docs) - Database of 3D protein structures.\n- [RCSB Protein Data Bank (PDB)](https://www.rcsb.org/) - Repository of 3D structural data of large biological molecules.\n- [Critical Assessment of Structure Prediction (CASP)](https://predictioncenter.org/) - Experiment for advancing the methods of predicting protein structure from sequence.\n- [Uniclust](https://uniclust.mmseqs.com/) - Collection of clustered protein sequence databases.\n- [CATH database](https://www.cathdb.info/) - Hierarchical classification of protein domain structures.\n### Genome\n- [Human Genome Resources at NCBI](https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml) - Database of image, proteomics, transcriptomics and systems biology.\n- [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) - Database of genetic sequence offered by NCBI.\n- [UCSC Genome Browser](https://genome.ucsc.edu/) - Genome blowser offered by UCSC.\n- [cBioPortal](https://www.cbioportal.org/) - Database of Cancer Genomics. This has overall metaview for a lot of patients.\n- [10x Genomics Dataset](https://www.10xgenomics.com/resources/datasets) - Collection of single-cell datasets.\n- [The Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/) - Resource for studying human gene expression and regulation.\n- [Dependency Map (DepMap)](https://depmap.org/portal/) - Genome-wide CRISPR-Cas9 screens in cancer cell lines.\n- [Catalogue Of Somatic Mutations In Cancer (COSMIC)](https://cancer.sanger.ac.uk/cosmic) - Comprehensive resource for exploring somatic mutations in human cancers.\n- [MGnify](https://www.ebi.ac.uk/metagenomics/) - Free resource for archiving, analysis, and browsing of metagenomic and metatranscriptomic data.\n- [JASPAR](http://jaspar.genereg.net/) - Open-access database of curated, non-redundant transcription factor binding profiles.\n### Disease\n- [KEGG DRUG](https://www.genome.jp/kegg/drug/) - Comprehensive drug information resource for approved drugs.\n- [DrugBank](https://www.drugbank.com/) - A database of drug and target maintained by the University of Alberta.\n### Interaction\n- Drug Gene Interaction\n  - [DGIdb](https://www.dgidb.org/) - A database of drug-gene interactions and the druggable genome.\n  - [Comparative Toxicogenomics Database](http://ctdbase.org/) - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.\n  - [SNAP](https://snap.stanford.edu/biodata/datasets/10002/10002-ChG-Miner.html#:~:text=Dataset%20information,or%20activation%20of%20the%20drug.) - A dataset which contains Drug-gene interactions. \n  - [Therapeutics Data Commons](https://tdcommons.ai/) - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.\n- Drug (-Cell line) Response\n  - [NCI60](https://dtp.cancer.gov/discovery_development/nci-60/) A database which focus on 60 cancer cell lines with many drugs.\n  - [Genomics of Drug Sensitivity in Cancer (GDSC)](https://www.cancerrxgene.org/) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.\n  - [Cancer Cell Line Encyclopedia](https://sites.broadinstitute.org/ccle/) - A database of cancer cell lines. This has 1000 cell lines.\n  - [CellMiner Cross Database (CellMinerCDB)](https://discover.nci.nih.gov/cellminercdb/) - Integration of multiple cancer cell line databases.\n- Chemical Protein Interaction\n  - [STITCH](http://stitch.embl.de/) - A database of Chemical Protein Interaction.\n  - [BindingDB](https://www.bindingdb.org/rwd/bind/index.jsp) - A database of compounds and targes.\n  - [PDBBind](http://www.pdbbind.org.cn/) - Database of experimentally measured binding affinity data for biomolecular complexes.\n  - [CrossDocked2020](https://arxiv.org/abs/2001.01037) - Large-scale dataset for machine learning in structure-based virtual screening.\n- Protein-Protein Interaction\n  - [STRING](https://string-db.org/) - Protein-Protein Interaction Networks for several organisms.\n  - [BioGRID](https://thebiogrid.org/) - Database of Protein, Genetic and Chemical Interactions.\n  - [HIPPIE](http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/) - Human Protein-Protein Interaction database.\n- Knowledge Graph\n  - [Drug Mechanism Database (DrugMechDB)](https://github.com/SuLab/DrugMechDB/tree/2.0.1): database of the mechanism of action from a drug to a disease.\n  - [DRKG](https://github.com/gnn4dr/DRKG) - A library for biological knowledge graph.\n### Clinical Trial\n- [ClinicalTrials.gov](https://clinicaltrials.gov/) - Database of privately and publicly funded clinical studies.\n- [ICD10](https://icd.who.int/browse10/2019/en) - International Classification of Diseases, 10th revision.\n- [EU Drug Regulating Authorities Clinical Trials DB (EudraCT)](https://eudract.ema.europa.eu/) - European database of clinical trials.\n- [MIMIC-IV](https://mimic.mit.edu/) - Freely accessible critical care database.\n \n## API\n- [PubMed esearch](https://www.nlm.nih.gov/dataguide/edirect/esearch.html): API for searching articles in PubMed.\n\n## Preprocess\n\n- [Chemistry Development Kit](https://github.com/cdk/cdk) - A software of cheminformatics and Machine Learning.\n- [RDKit](https://github.com/rdkit/rdkit) - A software of cheminformatics and Machine Learning.\n- [Scanpy](https://scanpy.readthedocs.io/en/stable/) - scRNA analysis library in Python.\n- [Seurat](https://satijalab.org/seurat/) - scRNA analysis library in R.\n\n## Machine Learning Tasks and Models\n\n## Drug Response Prediction\n- [drGAT](https://github.com/inoue0426/drGAT): A model for drug response prediction with gene explainability with attention mechanism.\n- [MOFGCN](https://github.com/weiba/MOFGCN/tree/main): GCN + heterogeneous network\n- [DeepDSC](https://ieeexplore-ieee-org.ezp2.lib.umn.edu/stamp/stamp.jsp?tp=\u0026arnumber=8723620\u0026tag=1): Autoencoder + Fully Connected NN\n- [DGDRP](https://github.com/minwoopak/heteronet): Multi-view embedding NN.\n- [DeepAEG](https://github.com/zhejiangzhuque/DeepAEG): GNN Embedding + Attention\n\n### Drug Repurposing\n\n- [DeepPurpose](https://github.com/kexinhuang12345/DeepPurpose) - A DL Library for Drug Repurposing. \n\n### Drug Target Interaction\n\n- [NeoDTI](https://github.com/FangpingWan/NeoDTI) - A library for Drug Target Interaction.\n\n### Compound Protein Interaction\n\n- [MCPINN](https://github.com/mhlee0903/multi_channels_PINN) - A library for drug discovery using Compound Protein Interaction and Machine Learning.\n- [TransformerCPI](https://github.com/lifanchen-simm/transformerCPI) - A library for Compound Protein Interaction prediction using Transformer.\n\n### Pre-trained embedding\n\n- [Evolutionary Scale Modeling](https://github.com/facebookresearch/esm) - a library for protein embeddings.\n- [ChemBERTa-2](https://github.com/seyonechithrananda/bert-loves-chemistry) - a library for chemical embeddingg and prediction.\n\n### LLM for biology\n\n- [AI4Chem/ChemLLM-7B-Chat](https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) - LLM for chemical and molecule science\n- [BioGPT](https://github.com/microsoft/BioGPT) - LLM for Biomedical text generation\n- [GeneGPT](https://github.com/ncbi/GeneGPT) - LLM for biomedical information with several API.\n- [GenePT](https://github.com/yiqunchen/GenePT) - foundation LLM for single cell data\n- [scPRINT](https://github.com/cantinilab/scPRINT) - scPRINT is pretrained on 50M cells to denoise and perform zero imputation of any single cell RNAseq profile.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finoue0426%2Fawesome-computational-biology","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finoue0426%2Fawesome-computational-biology","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finoue0426%2Fawesome-computational-biology/lists"}