Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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MDAnalysis mdanalysis.org
Python library for analyzing and altering molecular dynamics simulation trajectories.
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MassBank massbank.jp
Open source databases and tools for mass spectrometry reference spectra.
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LIPID MAPS lipidmaps.org
Database of lipids.
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LINCS L1000 lincsproject.org
Gene expression profiles (978 landmark genes) for >20,000 chemical and genetic perturbations across cell lines.
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KEGG REST API kegg.jp
API for accessing KEGG pathways, compounds, genes, and reactions.
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BACE kaggle.com
Binary classification and regression dataset for β-secretase 1 (BACE-1) inhibitor binding affinity.
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JASPAR jaspar.genereg.net
Database of transcription factor binding profiles.
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Kinase Inhibitor Bioactivity Data (KIBA) janeliascicomp.github.io
Integrated bioactivity scores for kinase inhibitors combining Ki, Kd, and IC50 measurements.
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1000 Genomes Project internationalgenome.org
Reference panel of human genetic variation from 2,504 individuals across 26 populations.
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DeepDSC ieeexplore-ieee-org.ezp2.lib.umn.edu
Autoencoder + fully connected NN.
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Therapeutic Target Database idrblab.net
Drug-target, target-disease, and drug-disease datasets.
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ICD10 icd.who.int
International Classification of Diseases, 10th revision.
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Human Cell Atlas humancellatlas.org
Open global atlas of all cells in the human body.
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BioMedLM huggingface.co
2.7B parameter GPT-2-style language model trained exclusively on biomedical literature from PubMed for biomedical question answering and text generation.
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Virchow2 huggingface.co
632M-parameter pathology vision transformer pretrained on 3.1M whole-slide images with mixed-magnification self-supervision.
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Virchow huggingface.co
Million-slide digital pathology foundation model using a vision transformer and self-supervised distillation for tile-level pathology image representation.
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Phikon-v2 huggingface.co
Updated pathology foundation model for general-purpose histology feature extraction and transfer learning.
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Phikon huggingface.co
ViT-based pathology foundation model pretrained with iBOT self-supervision on TCGA whole-slide images.
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BiomedCLIP huggingface.co
CLIP-based vision-language foundation model for biomedical images and text trained on PubMed figure–caption pairs.
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Tahoe-100M huggingface.co
Giga-scale single-cell perturbation atlas with >100 million profiles from 50 cancer cell lines exposed to ~1,100 small molecules.
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TCGA virtual spatial transcriptomics atlas huggingface.co
DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: DeepSpot-M.
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HEST Xenium virtual spatial transcriptomics huggingface.co
DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: DeepSpot-M.
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Geneformer huggingface.co
Context-aware, attention-based deep learning model pretrained on a large corpus of single-cell transcriptomes.
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H-Optimus-1 huggingface.co
1.1B-parameter pathology foundation model trained on billions of histology images from more than one million slides and 800K+ patients.
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H-Optimus-0 huggingface.co
1.1B-parameter histopathology foundation model trained with self-supervised learning on a large multi-center slide corpus.
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UNI2-h huggingface.co
Billion-parameter histopathology vision foundation model for tile-level feature extraction and downstream computational pathology tasks.
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AI4Chem/ChemLLM-7B-Chat huggingface.co
LLM for chemical & molecular science.
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Human Phenotype Ontology (HPO) hpo.jax.org
Standardized vocabulary of phenotypic abnormalities in human disease, linking genes, variants, and clinical features.
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HMDB (Human Metabolome Database) hmdb.ca
Comprehensive database of small molecule metabolites found in the human body.
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The Genotype-Tissue Expression (GTEx) gtexportal.org
Human gene expression and regulation resource.
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MSigDB (Molecular Signatures Database) gsea-msigdb.org
Curated gene sets derived from pathways and biological processes.
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TRRUST v2 grnpedia.org
Manually curated database of human and mouse transcriptional regulatory interactions between transcription factors and their target genes, expanded with literature-derived evidence.
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DrugBank go.drugbank.com
Database of drugs and targets (University of Alberta).
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gnomAD gnomad.broadinstitute.org
Genome Aggregation Database; genetic variation from large-scale sequencing projects.
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MOFGCN github.com
GCN + heterogeneous network.
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Drug Mechanism Database (DrugMechDB) github.com
Mechanisms of action from drug to disease.
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Uni-Mol2 github.com
Scaled molecular pretraining model using atomic, graph, and 3D geometry features, with models up to 1.1B parameters pretrained on 800M conformations.
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Enformer github.com
Transformer model predicting gene expression from DNA sequence.
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KEGG PATHWAY genome.jp
Collection of pathway maps.
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KEGG DRUG genome.jp
Comprehensive, approved drug information.
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KEGG COMPOUND genome.jp
Collection of small molecules and biopolymers.
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QM9 figshare.com
Quantum chemistry properties for 134K stable small organic molecules computed at DFT level.
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Norman et al. 2019 CRISPRa Perturb-seq figshare.com
Large-scale CRISPR activation Perturb-seq in K562 cells spanning single-gene and combinatorial perturbations.
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FANTOM5 fantom.gsc.riken.jp
Functional annotation of mammalian genome; comprehensive atlas of active enhancers, promoters, and transcription start sites across human and mouse cell types.
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EU Drug Regulating Authorities Clinical Trials DB (EudraCT) eudract.ema.europa.eu
European clinical trial database.
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ENCODE encodeproject.org
Encyclopedia of DNA Elements; regulatory and functional genomic elements across the genome.
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MGnify ebi.ac.uk
Resource for metagenomic and metatranscriptomic data.
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Pfam ebi.ac.uk
Database of protein families described by multiple sequence alignments and hidden Markov models.
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InterPro ebi.ac.uk
Protein families, domains, and functional sites database integrating 14 member databases including Pfam and PROSITE.
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IntAct ebi.ac.uk
Open-source molecular interaction database and analysis system from EMBL-EBI.
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