Awesome Computational Biology Overview

Awesome list of computational biology.

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Awesome Computational Biology

A curated collection of databases, software, and papers related to computational biology.

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to the study of biological, ecological, behavioural, and social systems. — Wikipedia

Table of Contents

• Databases
  • scRNA
  • Compound
  • Pathway
  • Mass Spectra
  • Protein
  • Genome
  • Disease
  • Interaction
    • Drug-Gene Interaction
    • Drug (Cell Line) Response
    • Chemical-Protein Interaction
    • Protein-Protein Interaction
    • Knowledge Graph
  • Clinical Trial
• API
• Preprocessing Tools
• Machine Learning Tasks and Models
  • Drug Response Prediction
  • Drug Repurposing
  • Drug Target Interaction
  • Compound-Protein Interaction
  • Pre-trained Embedding
  • LLM for Biology
  • Foundation Models

Databases

scRNA

• Gene Expression Omnibus — Public functional genomics database.
• Single Cell PORTAL — Public database for single-cell RNA.
• Single Cell Expression Atlas — Public database for single-cell RNA.

Compound

• PubChem — One of the largest chemical databases (compounds, genes, and proteins).
• ChEBI — Database focused on small chemical compounds.
• ChEMBL — Bioactive molecules with drug-like properties.
• ChemSpider — Chemical structure database.
• KEGG COMPOUND — Collection of small molecules and biopolymers.
• LIPID MAPS — Database of lipids.
• Rhea — Database of chemical reactions.
• Drug Repurposing Hub — Collections of drug repurposing data (drug, MoA, target, etc).
• Therapeutic Target Database — Drug-target, target-disease, and drug-disease datasets.
• ZINC ligand discovery database — Free database of commercially-available compounds for virtual screening.
• MoleculeNet — Benchmark datasets for molecular machine learning.

Pathway

• PathwayCommons — Database of pathways and interactions.
• KEGG PATHWAY — Collection of pathway maps.
• WikiPathways — Database of biological pathways.
• 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.

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).
• PROTEIN DATA BANK (PDB) — 3D structures of proteins, nucleic acids, complexes.
• UniProt — Functional information on proteins.
• AlphaFold Protein Structure Database — 3D protein structure predictions.
• RCSB Protein Data Bank — Repository for structural data of biological molecules.
• 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

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

Disease

• KEGG DRUG — Comprehensive, approved drug information.
• DrugBank — Database of drugs and targets (University of Alberta).

Interaction

Drug-Gene Interaction

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

Drug (Cell Line) Response

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

Chemical-Protein Interaction

• STITCH — Chemical-protein interactions.
• BindingDB — Compounds and target database.
• PDBBind — Binding affinity data for biomolecular complexes.
• CrossDocked2020 — Large-scale dataset for structure-based virtual screening.

Protein-Protein Interaction

• STRING — PPI networks for multiple organisms.
• BioGRID — Protein, genetic, and chemical interactions.
• HIPPIE — Human protein-protein interaction database.

Knowledge Graph

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

Clinical Trial

• 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.

API

• 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.

Preprocessing Tools

• Chemistry Development Kit (⭐568) — Cheminformatics software & machine learning tools.
• FlashDeconv (⭐10) — High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min).
• RDKit (⭐3.3k) — Cheminformatics software & machine learning toolkit.
• ChatSpatial (⭐11) — MCP server for spatial transcriptomics analysis via natural language.
• Scanpy — Python library for scRNA-seq analysis.
• Seurat — R library for scRNA-seq analysis.
• Squidpy — Python library for spatial single-cell analysis.

Machine Learning Tasks and Models

Drug Response Prediction

• drGAT (⭐1) — Attention-based model for drug response prediction with gene explainability.
• MOFGCN (⭐6) — GCN + heterogeneous network.
• DeepDSC — Autoencoder + fully connected NN.
• DGDRP (⭐0) — Multi-view embedding neural network.
• DeepAEG (⭐3) — GNN embedding + attention mechanism.

Drug Repurposing

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

Drug Target Interaction

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

Compound-Protein Interaction

• MCPINN (⭐3) — Drug discovery via compound-protein interaction and machine learning.
• TransformerCPI (⭐152) — CPI prediction using Transformer.

Pre-trained Embedding

• Evolutionary Scale Modeling (ESM) (⭐4k) — Protein embeddings.
• ChemBERTa-2 (⭐486) — Chemical embeddings & prediction.

LLM for Biology

• AI4Chem/ChemLLM-7B-Chat — LLM for chemical & molecular science.
• BioGPT (⭐4.5k) — LLM for biomedical text generation.
• GeneGPT (⭐420) — LLM for biomedical information, integrated with various APIs.
• GenePT (⭐308) — Foundation LLM for single-cell data.
• scPRINT (⭐138) — Pretrained on 50M cells for scRNA-seq denoising & zero imputation.

Foundation Models

• 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.