Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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ChEMBL ebi.ac.uk
Bioactive molecules with drug-like properties.
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ChEBI ebi.ac.uk
Database focused on small chemical compounds.
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DUD-E (Directory of Useful Decoys, Enhanced) dude.docking.org
Structure-based virtual screening benchmark with active ligands and challenging decoy sets across diverse protein targets.
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NCI60 dtp.cancer.gov
Focuses on 60 cancer cell lines and many drugs.
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DrugTargetCommons drugtargetcommons.fimm.fi
Community platform for curating and integrating experimental bioactivity data across drugs and targets.
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DrugCentral drugcentral.org
Online drug compendium with drug mode of action and indication information.
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CLM-X doi.org
Multi-way Transformer foundation model jointly handling RNA-only, ATAC-only, and paired RNA–ATAC single-cell inputs for integration, translation, annotation, and perturbation prediction.
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EXPRESSO doi.org
Supervised treatment-response framework using pretreatment tumor transcriptomics, drug targets, and context-specific biomarkers across multiple cancer types and therapies.
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Atacformer doi.org
Transformer foundation model for scATAC-seq that learns embeddings of cis-regulatory elements for clustering, annotation, and reference mapping.
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MutationProjector doi.org
Pan-cancer genotype foundation model trained on mutations and copy-number alterations from >30K tumors for clinical representation learning.
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SCARF doi.org
Single-cell RNA+ATAC foundation model pretrained on >2.7M cells for multimodal representation, matching, cross-omics translation, and few-shot annotation.
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EpiFoundation doi.org
Foundation model for scATAC-seq using peak-to-gene aligned pretraining for cell representation, annotation, batch correction, and gene-expression prediction.
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HiCFoundation doi.org
Hi-C foundation model pretrained on large-scale chromatin-contact maps for 3D-genome analysis, epigenomic prediction, and single-cell Hi-C adaptation.
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CAPTAIN doi.org
Multimodal foundation model pretrained on co-assayed single-cell RNA and protein for joint representation learning and cross-modal downstream tasks.
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DTLCDR doi.org
Target-based multimodal framework for preclinical cancer drug response prediction and transfer to clinical response, with explicit unseen-drug generalization.
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DisGeNET disgenet.org
Database of gene-disease associations integrating expert-curated and GWAS data.
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DISEASES diseases.jensenlab.org
Gene–disease association database integrating evidence from text mining, curated databases, and experimental data.
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CellMiner Cross Database (CellMinerCDB) discover.nci.nih.gov
Integrates multiple cancer cell line databases.
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DGIdb dgidb.org
Drug-gene interactions and the druggable genome.
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PRISM depmap.org
Cancer drug sensitivity profiling of >4,500 drugs across >900 cancer cell lines using pooled-cell-line barcoding.
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Dependency Map (DepMap) depmap.org
CRISPR-Cas9 screens in cancer cell lines.
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DeepSEA deepsea.princeton.edu
Deep learning framework for predicting chromatin effects of sequence alterations with single-nucleotide sensitivity across thousands of chromatin features.
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Monocle3 cole-trapnell-lab.github.io
Single-cell trajectory analysis tool for learning developmental trajectories and ordering cells in pseudotime.
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ClinicalTrials.gov API clinicaltrials.gov
API for querying clinical trial metadata and results.
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ClinicalTrials.gov clinicaltrials.gov
Privately and publicly funded clinical studies.
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ChemSpider chemspider.com
Chemical structure database.
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CZ CELLxGENE cellxgene.cziscience.com
Single-cell dataset repository and interactive explorer from the Chan Zuckerberg Initiative.
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HIPPIE cbdm-01.zdv.uni-mainz.de
Human protein-protein interaction database.
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CATH database cathdb.info
Hierarchical classification of protein domain structures.
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Genomics of Drug Sensitivity in Cancer (GDSC) cancerrxgene.org
Drug sensitivity for ~1000 human cancer cell lines and hundreds of compounds.
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Catalogue Of Somatic Mutations In Cancer (COSMIC) cancer.sanger.ac.uk
Resource on somatic mutations in cancers.
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The Cancer Genome Atlas (TCGA) cancer.gov
Comprehensive multi-omics (genomics, transcriptomics, proteomics, methylation) dataset for 33 cancer types across ~11,000 patients.
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BEAT AML biodev.github.io
Functional ex vivo drug sensitivity measurements paired with genomics for acute myeloid leukemia.
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BioCyc biocyc.org
Collection of pathway/genome databases across thousands of organisms.
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BindingDB bindingdb.org
Compounds and target database.
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BindingDB Curated Sets bindingdb.org
Curated binding affinity datasets for protein–ligand interaction benchmarking.
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Bison arxiv.org
Cross-dataset model for globally unseen-compound response prediction using a shared gene representation, discrete diffusion models, and matched drug-contrast supervision.
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PerturbRx arxiv.org
Treatment-conditioned representation learning framework that transfers drug-induced latent transitions learned from single-cell perturbation data to patient-level cancer treatment-response prediction.
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CrossDocked2020 arxiv.org
Large-scale dataset for structure-based virtual screening.
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AlphaFold Protein Structure Database alphafold.ebi.ac.uk
3D protein structure predictions.
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10x Genomics Dataset 10xgenomics.com
Collection of single-cell datasets.
