116 lines
7.3 KiB
Plaintext
116 lines
7.3 KiB
Plaintext
# Awesome Computational Biology [](https://awesome.re)
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A knowledge collection of databases, software and papers related to computational biology.
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> Computational biology involves the development and application of data-analytical and theoretical methods,
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> mathematical modelling and computational simulation techniques to the study of biological, ecological,
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> behavioural, and social systems. - [Wikipedia](https://en.wikipedia.org/wiki/Computational_biology)
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## Contents
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- [Databases](#databases)
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- [scRNA](#scrna)
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- [Compound](#compound)
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- [Pathway](#pathway)
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- [Mass Spectra](#mass-spectra)
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- [Protein](#protein)
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- [Genome](#genome)
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- [Disease](#disease)
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- [Interaction](#interaction)
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- [Preprocess](#preprocess)
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- [Machine Learning Tasks and Models](#machine-learning-tasks-and-models)
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- [Drug Repurposing](#drug-repurposing)
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- [Drug Target Interaction](#drug-target-interaction)
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- [Compound Protein Interaction](#compound-protein-interaction)
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- [Pre-trained embedding](#pre-trained-embedding)
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- [LLM for biology](#llm-for-biology)
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## Databases
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### scRNA
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- [Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/) - Public functional genemics database.
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- [Single Cell PORTAL](https://singlecell.broadinstitute.org/single_cell) - Public database for single cell RNA.
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- [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc/home) - Public database for single cell RNA.
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### Compound
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- [PubChem](https://pubchem.ncbi.nlm.nih.gov/) - One of the biggest chemical database such as compounds, genes and proteins.
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- [ChEBI](https://www.ebi.ac.uk/chebi/) - Chemical database focused on small chemical compounds.
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- [ChEMBL](https://www.ebi.ac.uk/chembl/) - Database of bioactive molecules with drug-like properties.
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- [ChemSpider](http://www.chemspider.com/) - Chemical structure database.
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- [KEGG COMPOUND](https://www.genome.jp/kegg/compound/) - Collection of small molecules and biopolymers.
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- [LIPID MAPS](https://www.lipidmaps.org/databases/lmsd/overview) - Database of lipids.
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- [Rhea](https://www.rhea-db.org/) - Database of chemical reactions.
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- [Drug Repurposing Hub](https://repo-hub.broadinstitute.org/repurposing#download-data) - Collections of drug repurposing data containing drug, moa, target etc.
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### Pathway
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- [PathwayCommons](https://www.pathwaycommons.org/) - Database of Pathways and Interactions.
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- [KEGG PATHWAY](https://www.genome.jp/kegg/pathway.html) - Collection fo drawn pathway maps.
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- [WikiPathways](https://wikipathways.org/) - Database of biological pathways.
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### Mass Spectra
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- [MassBank](http://www.massbank.jp/) - Open souce databases and tools for mass spectrometry reference spectra.
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- [MoNA MassBank of North America](https://mona.fiehnlab.ucdavis.edu/) - Meta database of metabolite mass spectra, metadata and associated compounds.
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### Protein
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- [THE HUMAN PROTEIN ATLAS](https://www.proteinatlas.org/) - One of the biggest human protein database contained cells, tissues, and organs.
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- [PROTEIN DATA BANK](https://www.rcsb.org/) - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.
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- [UniProt](https://www.uniprot.org/) - The collection of functional information on proteins.
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- [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/api-docs) - Database of 3D protein structures.
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### Genome
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- [Human Genome Resources at NCBI](https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml) - Database of image, proteomics, transcriptomics and systems biology.
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- [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) - Database of genetic sequence offered by NCBI.
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- [UCSC Genome Browser](https://genome.ucsc.edu/) - Genome blowser offered by UCSC.
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- [cBioPortal](https://www.cbioportal.org/) - Database of Cancer Genomics. This has overall metaview for a lot of patients.
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### Disease
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- [KEGG DRUG](https://www.genome.jp/kegg/drug/) - Comprehensive drug information resource for approved drugs.
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- [DrugBank](https://www.drugbank.com/) - A database of drug and target maintained by the University of Alberta.
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### Interaction
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- Drug Gene Interaction
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- [DGIdb](https://www.dgidb.org/) - A database of drug-gene interactions and the druggable genome.
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- [Comparative Toxicogenomics Database](http://ctdbase.org/) - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
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- [SNAP](https://snap.stanford.edu/biodata/datasets/10002/10002-ChG-Miner.html#:~:text=Dataset%20information,or%20activation%20of%20the%20drug.) - A dataset which contains Drug-gene interactions.
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- [Comparative Toxicogenomics Database](https://ctdbase.org/) - A database for drug-target interactions.
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- [Therapeutics Data Commons](https://tdcommons.ai/) - A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction.
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- Drug (-Cell line) Response
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- [NCI60](https://dtp.cancer.gov/discovery_development/nci-60/) A database which focus on 60 cancer cell lines with many drugs.
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- [Genomics of Drug Sensitivity in Cancer (GDSC)](https://www.cancerrxgene.org/) - A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds.
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- [Cancer Cell Line Encyclopedia](https://sites.broadinstitute.org/ccle/) - A database of cancer cell lines. This has 1000 cell lines.
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- Chemical Protein Interaction
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- [STITCH](http://stitch.embl.de/) - A database of Chemical Protein Interaction.
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- [BindingDB](https://www.bindingdb.org/rwd/bind/index.jsp) - A database of compounds and targes.
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- Protein-Protein Interaction
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- [STRING](https://string-db.org/) - Protein-Protein Interaction Networks for several organisms.
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- [BioGRID](https://thebiogrid.org/) - Database of Protein, Genetic and Chemical Interactions.
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- [HIPPIE](http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/) - Human Protein-Protein Interaction database.
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## Preprocess
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- [Chemistry Development Kit](https://github.com/cdk/cdk) - A software of cheminformatics and Machine Learning.
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- [RDKit](https://github.com/rdkit/rdkit) - A software of cheminformatics and Machine Learning.
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- [Scanpy](https://scanpy.readthedocs.io/en/stable/) - scRNA analysis library in Python.
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- [Seurat](https://satijalab.org/seurat/) - scRNA analysis library in R.
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## Machine Learning Tasks and Models
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### Drug Repurposing
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- [DeepPurpose](https://github.com/kexinhuang12345/DeepPurpose) - A DL Library for Drug Repurposing and so on.
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- [DRKG](https://github.com/gnn4dr/DRKG) - A library for biological knowledge graph.
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### Drug Target Interaction
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- [NeoDTI](https://github.com/FangpingWan/NeoDTI) - A library for Drug Target Interaction.
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### Compound Protein Interaction
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- [MCPINN](https://github.com/mhlee0903/multi_channels_PINN) - A library for drug discovery using Compound Protein Interaction and Machine Learning.
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- [TransformerCPI](https://github.com/lifanchen-simm/transformerCPI) - A library for Compound Protein Interaction prediction using Transformer.
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### Pre-trained embedding
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- [Evolutionary Scale Modeling](https://github.com/facebookresearch/esm) - a library for protein embeddings.
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- [ChemBERTa-2](https://github.com/seyonechithrananda/bert-loves-chemistry) - a library for chemical embeddingg and prediction.
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### LLM for biology
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- [AI4Chem/ChemLLM-7B-Chat](https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) - LLM for chemical and molecule science
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- [BioGPT](https://github.com/microsoft/BioGPT) - LLM for Biomedical text generation
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