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Awesome list of computational biology.

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[ Daily / Weekly / Overview ]

Aug 26 - Sep 01, 2024

Databases / Compound

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

• MoleculeNet - Benchmark for molecular machine learning.

• Ames Mutagenicity dataset - Dataset for predicting mutagenicity.

• ADCdb - Database for antibody-drug conjugates.

Databases / Protein

• RCSB Protein Data Bank (PDB) - Repository of 3D structural data of large biological molecules.

• Critical Assessment of Structure Prediction (CASP) - Experiment for advancing the methods of predicting protein structure from sequence.

• Uniclust - Collection of clustered protein sequence databases.

• CATH database - Hierarchical classification of protein domain structures.

Databases / Genome

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

• The Genotype-Tissue Expression (GTEx) - Resource for studying human gene expression and regulation.

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

• Catalogue Of Somatic Mutations In Cancer (COSMIC) - Comprehensive resource for exploring somatic mutations in human cancers.

• MGnify - Free resource for archiving, analysis, and browsing of metagenomic and metatranscriptomic data.

• JASPAR - Open-access database of curated, non-redundant transcription factor binding profiles.

Databases / Clinical Trial

• ClinicalTrials.gov - Database of privately and publicly funded clinical studies.

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

• EU Drug Regulating Authorities Clinical Trials DB (EudraCT) - European database of clinical trials.

• MIMIC-IV - Freely accessible critical care database.

Aug 05 - Aug 11, 2024

Databases / Compound

• Therapeutic Target Database - collections of drug-target, target-disease, and drug-disease dataset.

Drug Response Prediction / LLM for biology

• scPRINT (⭐10) - scPRINT is pretrained on 50M cells to denoise and perform zero imputation of any single cell RNAseq profile.

Jul 15 - Jul 21, 2024

Databases / Interaction

• Knowledge Graph
  • Drug Mechanism Database (DrugMechDB) (⭐54): database of the mechanism of action from a drug to a disease.
  • DRKG (⭐574) - A library for biological knowledge graph.

API / Clinical Trial

• PubMed esearch: API for searching articles in PubMed.

Drug Response Prediction / Clinical Trial

• drGAT (⭐2): A model for drug response prediction with gene explainability with attention mechanism.

Drug Response Prediction / LLM for biology

• GeneGPT (⭐366) - LLM for biomedical information with several API.

• GenePT (⭐164) - foundation LLM for single cell data

Mar 11 - Mar 17, 2024

Drug Response Prediction / Pre-trained embedding

• Evolutionary Scale Modeling (⭐3.1k) - a library for protein embeddings.

• ChemBERTa-2 (⭐383) - a library for chemical embeddingg and prediction.

Drug Response Prediction / LLM for biology

• AI4Chem/ChemLLM-7B-Chat - LLM for chemical and molecule science

• BioGPT (⭐4.3k) - LLM for Biomedical text generation

Nov 27 - Dec 03, 2023

Databases / Compound

• Drug Repurposing Hub - Collections of drug repurposing data containing drug, moa, target etc.

Databases / Protein

• AlphaFold Protein Structure Database - Database of 3D protein structures.

Databases / Interaction

• Protein-Protein Interaction
  • STRING - Protein-Protein Interaction Networks for several organisms.
  • BioGRID - Database of Protein, Genetic and Chemical Interactions.
  • HIPPIE - Human Protein-Protein Interaction database.

Sep 04 - Sep 10, 2023

Databases / Compound

• Rhea - Database of chemical reactions.

Jun 12 - Jun 18, 2023

Databases / scRNA

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

Databases / Pathway

• PathwayCommons - Database of Pathways and Interactions.

Databases / Genome

• cBioPortal - Database of Cancer Genomics. This has overall metaview for a lot of patients.

Preprocess / Clinical Trial

• Scanpy - scRNA analysis library in Python.

• Seurat - scRNA analysis library in R.

Apr 17 - Apr 23, 2023

Databases / scRNA

• Gene Expression Omnibus - Public functional genemics database.

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

Dec 26 - Jan 01, 2022

Databases / Interaction

• Drug (-Cell line) Response
  • NCI60 A database which focus on 60 cancer cell lines with many drugs.
  • Genomics of Drug Sensitivity in Cancer (GDSC) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.
  • Cancer Cell Line Encyclopedia - A database of cancer cell lines. This has 1000 cell lines.
  • CellMiner Cross Database (CellMinerCDB) - Integration of multiple cancer cell line databases.

May 16 - May 22, 2022

Databases / Compound

• ChEBI - Chemical database focused on small chemical compounds.

Databases / Protein

• PROTEIN DATA BANK - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.

May 09 - May 15, 2022

Databases / Compound

• PubChem - One of the biggest chemical database such as compounds, genes and proteins.

• ChEMBL - Database of bioactive molecules with drug-like properties.

• ChemSpider - Chemical structure database.

• KEGG COMPOUND - Collection of small molecules and biopolymers.

• LIPID MAPS - Database of lipids.

Databases / Pathway

• KEGG PATHWAY - Collection fo drawn pathway maps.

• WikiPathways - Database of biological pathways.

Databases / Mass Spectra

• MassBank - Open souce databases and tools for mass spectrometry reference spectra.

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

Databases / Protein

• THE HUMAN PROTEIN ATLAS - One of the biggest human protein database contained cells, tissues, and organs.

• UniProt - The collection of functional information on proteins.

Databases / Genome

• Human Genome Resources at NCBI - Database of image, proteomics, transcriptomics and systems biology.

• GenBank - Database of genetic sequence offered by NCBI.

• UCSC Genome Browser - Genome blowser offered by UCSC.

Databases / Disease

• KEGG DRUG - Comprehensive drug information resource for approved drugs.

Preprocess / Clinical Trial

• Chemistry Development Kit (⭐486) - A software of cheminformatics and Machine Learning.

• RDKit (⭐2.6k) - A software of cheminformatics and Machine Learning.

Drug Response Prediction / Drug Repurposing

• DeepPurpose (⭐947) - A DL Library for Drug Repurposing.

Drug Response Prediction / Drug Target Interaction

• NeoDTI (⭐73) - A library for Drug Target Interaction.

Drug Response Prediction / Compound Protein Interaction

• MCPINN (⭐3) - A library for drug discovery using Compound Protein Interaction and Machine Learning.

• TransformerCPI (⭐133) - A library for Compound Protein Interaction prediction using Transformer.

Feb 21 - Feb 27, 2022

Databases / Disease

• DrugBank - A database of drug and target maintained by the University of Alberta.

Databases / Interaction

• Drug Gene Interaction
  • DGIdb - A database of drug-gene interactions and the druggable genome.
  • Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
  • SNAP - A dataset which contains Drug-gene interactions.
  • Therapeutics Data Commons - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.

• Chemical Protein Interaction
  • STITCH - A database of Chemical Protein Interaction.
  • BindingDB - A database of compounds and targes.
  • PDBBind - Database of experimentally measured binding affinity data for biomolecular complexes.
  • CrossDocked2020 - Large-scale dataset for machine learning in structure-based virtual screening.