awesome-computational-biology
Awesome list of computational biology.
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awesomeawesome-listcomputational-biologydrug-discoverydrug-repurposingmachine-learning
Awesome Computational Biology / Databases / scRNA | |||
| Gene Expression Omnibus | Public functional genemics database | ||
| Single Cell PORTAL | Public database for single cell RNA | ||
| Single Cell Expression Atlas | Public database for single cell RNA | ||
Awesome Computational Biology / Databases / Compound | |||
| PubChem | One of the biggest chemical database such as compounds, genes and proteins | ||
| ChEBI | Chemical database focused on small chemical compounds | ||
| 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 | ||
| Rhea | Database of chemical reactions | ||
| Drug Repurposing Hub | Collections of drug repurposing data containing drug, moa, target etc | ||
| Therapeutic Target Database | collections of drug-target, target-disease, and drug-disease dataset | ||
| 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 | ||
Awesome Computational Biology / Databases / Pathway | |||
| PathwayCommons | Database of Pathways and Interactions | ||
| KEGG PATHWAY | Collection fo drawn pathway maps | ||
| WikiPathways | Database of biological pathways | ||
Awesome Computational Biology / 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 | ||
Awesome Computational Biology / Databases / Protein | |||
| THE HUMAN PROTEIN ATLAS | One of the biggest human protein database contained cells, tissues, and organs | ||
| PROTEIN DATA BANK | Database of the 3D shapes of proteins, nucleic acids, and complex assemblies | ||
| UniProt | The collection of functional information on proteins | ||
| AlphaFold Protein Structure Database | Database of 3D protein structures | ||
| 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 | ||
Awesome Computational Biology / 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 | ||
| cBioPortal | Database of Cancer Genomics. This has overall metaview for a lot of patients | ||
| 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 | ||
Awesome Computational Biology / Databases / Disease | |||
| KEGG DRUG | Comprehensive drug information resource for approved drugs | ||
| DrugBank | A database of drug and target maintained by the University of Alberta | ||
Awesome Computational Biology / 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 | ||
Awesome Computational Biology / 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 | ||
Awesome Computational Biology / Databases / 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 | ||
Awesome Computational Biology / 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 | ||
Awesome Computational Biology / Databases / Interaction / Knowledge Graph | |||
| Drug Mechanism Database (DrugMechDB) | 54 | about 1 year ago | : database of the mechanism of action from a drug to a disease |
| DRKG | 576 | over 2 years ago | A library for biological knowledge graph |
Awesome Computational Biology / 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 | ||
Awesome Computational Biology / API | |||
| PubMed esearch | : API for searching articles in PubMed | ||
Awesome Computational Biology / Preprocess | |||
| Chemistry Development Kit | 493 | 16 days ago | A software of cheminformatics and Machine Learning |
| RDKit | 2,599 | 9 days ago | A software of cheminformatics and Machine Learning |
| Scanpy | scRNA analysis library in Python | ||
| Seurat | scRNA analysis library in R | ||
Awesome Computational Biology / Drug Response Prediction | |||
| drGAT | 2 | about 1 month ago | : A model for drug response prediction with gene explainability with attention mechanism |
Awesome Computational Biology / Drug Response Prediction / Drug Repurposing | |||
| DeepPurpose | 958 | 4 months ago | A DL Library for Drug Repurposing |
Awesome Computational Biology / Drug Response Prediction / Drug Target Interaction | |||
| NeoDTI | 73 | over 3 years ago | A library for Drug Target Interaction |
Awesome Computational Biology / Drug Response Prediction / Compound Protein Interaction | |||
| MCPINN | 3 | about 1 year ago | A library for drug discovery using Compound Protein Interaction and Machine Learning |
| TransformerCPI | 133 | over 2 years ago | A library for Compound Protein Interaction prediction using Transformer |
Awesome Computational Biology / Drug Response Prediction / Pre-trained embedding | |||
| Evolutionary Scale Modeling | 3,148 | 8 months ago | a library for protein embeddings |
| ChemBERTa-2 | 392 | almost 2 years ago | a library for chemical embeddingg and prediction |
Awesome Computational Biology / Drug Response Prediction / LLM for biology | |||
| AI4Chem/ChemLLM-7B-Chat | LLM for chemical and molecule science | ||
| BioGPT | 4,288 | 2 months ago | LLM for Biomedical text generation |
| GeneGPT | 373 | 8 months ago | LLM for biomedical information with several API |
| GenePT | 166 | 7 months ago | foundation LLM for single cell data |
| scPRINT | 11 | 12 days ago | scPRINT is pretrained on 50M cells to denoise and perform zero imputation of any single cell RNAseq profile |
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