202 lines
9.0 KiB
HTML
202 lines
9.0 KiB
HTML
<h1 id="awesome-computational-biology-awesome">Awesome Computational
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Biology <a href="https://awesome.re"><img
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src="https://awesome.re/badge.svg" alt="Awesome" /></a></h1>
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<p>A knowledge collection of databases, software and papers related to
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computational biology.</p>
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<blockquote>
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<p>Computational biology involves the development and application of
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data-analytical and theoretical methods, mathematical modelling and
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computational simulation techniques to the study of biological,
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ecological, behavioural, and social systems. - <a
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href="https://en.wikipedia.org/wiki/Computational_biology">Wikipedia</a></p>
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</blockquote>
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<h2 id="contents">Contents</h2>
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<ul>
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<li><a href="#databases">Databases</a>
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<ul>
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<li><a href="#scrna">scRNA</a></li>
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<li><a href="#compound">Compound</a></li>
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<li><a href="#pathway">Pathway</a></li>
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<li><a href="#mass-spectra">Mass Spectra</a></li>
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<li><a href="#protein">Protein</a></li>
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<li><a href="#genome">Genome</a></li>
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<li><a href="#disease">Disease</a></li>
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<li><a href="#interaction">Interaction</a></li>
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</ul></li>
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<li><a href="#preprocess">Preprocess</a></li>
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<li><a href="#machine-learning-tasks-and-models">Machine Learning Tasks
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and Models</a>
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<ul>
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<li><a href="#drug-repurposing">Drug Repurposing</a></li>
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<li><a href="#drug-target-interaction">Drug Target Interaction</a></li>
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<li><a href="#compound-protein-interaction">Compound Protein
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Interaction</a></li>
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<li><a href="#pre-trained-embedding">Pre-trained embedding</a></li>
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<li><a href="#llm-for-biology">LLM for biology</a></li>
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</ul></li>
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</ul>
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<h2 id="databases">Databases</h2>
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<h3 id="scrna">scRNA</h3>
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<ul>
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<li><a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression
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Omnibus</a> - Public functional genemics database.</li>
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<li><a href="https://singlecell.broadinstitute.org/single_cell">Single
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Cell PORTAL</a> - Public database for single cell RNA.</li>
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<li><a href="https://www.ebi.ac.uk/gxa/sc/home">Single Cell Expression
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Atlas</a> - Public database for single cell RNA. ### Compound</li>
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<li><a href="https://pubchem.ncbi.nlm.nih.gov/">PubChem</a> - One of the
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biggest chemical database such as compounds, genes and proteins.</li>
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<li><a href="https://www.ebi.ac.uk/chebi/">ChEBI</a> - Chemical database
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focused on small chemical compounds.</li>
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<li><a href="https://www.ebi.ac.uk/chembl/">ChEMBL</a> - Database of
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bioactive molecules with drug-like properties.</li>
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<li><a href="http://www.chemspider.com/">ChemSpider</a> - Chemical
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structure database.</li>
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<li><a href="https://www.genome.jp/kegg/compound/">KEGG COMPOUND</a> -
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Collection of small molecules and biopolymers.</li>
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<li><a href="https://www.lipidmaps.org/databases/lmsd/overview">LIPID
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MAPS</a> - Database of lipids.</li>
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<li><a href="https://www.rhea-db.org/">Rhea</a> - Database of chemical
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reactions.</li>
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<li><a
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href="https://repo-hub.broadinstitute.org/repurposing#download-data">Drug
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Repurposing Hub</a> - Collections of drug repurposing data containing
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drug, moa, target etc. ### Pathway</li>
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<li><a href="https://www.pathwaycommons.org/">PathwayCommons</a> -
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Database of Pathways and Interactions.</li>
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<li><a href="https://www.genome.jp/kegg/pathway.html">KEGG PATHWAY</a> -
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Collection fo drawn pathway maps.</li>
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<li><a href="https://wikipathways.org/">WikiPathways</a> - Database of
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biological pathways. ### Mass Spectra</li>
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<li><a href="http://www.massbank.jp/">MassBank</a> - Open souce
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databases and tools for mass spectrometry reference spectra.</li>
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<li><a href="https://mona.fiehnlab.ucdavis.edu/">MoNA MassBank of North
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America</a> - Meta database of metabolite mass spectra, metadata and
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associated compounds. ### Protein</li>
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<li><a href="https://www.proteinatlas.org/">THE HUMAN PROTEIN ATLAS</a>
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- One of the biggest human protein database contained cells, tissues,
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and organs.</li>
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<li><a href="https://www.rcsb.org/">PROTEIN DATA BANK</a> - Database of
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the 3D shapes of proteins, nucleic acids, and complex assemblies.</li>
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<li><a href="https://www.uniprot.org/">UniProt</a> - The collection of
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functional information on proteins.</li>
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<li><a href="https://alphafold.ebi.ac.uk/api-docs">AlphaFold Protein
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Structure Database</a> - Database of 3D protein structures. ###
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Genome</li>
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<li><a
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href="https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml">Human
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Genome Resources at NCBI</a> - Database of image, proteomics,
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transcriptomics and systems biology.</li>
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<li><a href="https://www.ncbi.nlm.nih.gov/genbank/">GenBank</a> -
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Database of genetic sequence offered by NCBI.</li>
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<li><a href="https://genome.ucsc.edu/">UCSC Genome Browser</a> - Genome
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blowser offered by UCSC.</li>
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<li><a href="https://www.cbioportal.org/">cBioPortal</a> - Database of
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Cancer Genomics. This has overall metaview for a lot of patients. ###
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Disease</li>
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<li><a href="https://www.genome.jp/kegg/drug/">KEGG DRUG</a> -
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Comprehensive drug information resource for approved drugs.</li>
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<li><a href="https://www.drugbank.com/">DrugBank</a> - A database of
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drug and target maintained by the University of Alberta. ###
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Interaction</li>
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<li>Drug Gene Interaction
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<ul>
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<li><a href="https://www.dgidb.org/">DGIdb</a> - A database of drug-gene
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interactions and the druggable genome.</li>
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<li><a href="http://ctdbase.org/">Comparative Toxicogenomics
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Database</a> - A database of Chemical-gene interactions,
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Chemical-disease associations, Gene-disease associations, and
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Chemical-phenotype associations.</li>
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<li><a
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href="https://snap.stanford.edu/biodata/datasets/10002/10002-ChG-Miner.html#:~:text=Dataset%20information,or%20activation%20of%20the%20drug.">SNAP</a>
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- A dataset which contains Drug-gene interactions.</li>
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<li><a href="https://ctdbase.org/">Comparative Toxicogenomics
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Database</a> - A database for drug-target interactions.</li>
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<li><a href="https://tdcommons.ai/">Therapeutics Data Commons</a> - A
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database for a lot of tasks such as drug-target, drug-response,
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drug-drug interaction.</li>
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</ul></li>
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<li>Drug (-Cell line) Response
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<ul>
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<li><a
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href="https://dtp.cancer.gov/discovery_development/nci-60/">NCI60</a> A
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database which focus on 60 cancer cell lines with many drugs.</li>
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<li><a href="https://www.cancerrxgene.org/">Genomics of Drug Sensitivity
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in Cancer (GDSC)</a> - A database of drug sensitibity which has 1000
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human cancer cell lines and 100s compounds.</li>
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<li><a href="https://sites.broadinstitute.org/ccle/">Cancer Cell Line
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Encyclopedia</a> - A database of cancer cell lines. This has 1000 cell
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lines.</li>
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</ul></li>
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<li>Chemical Protein Interaction
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<ul>
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<li><a href="http://stitch.embl.de/">STITCH</a> - A database of Chemical
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Protein Interaction.</li>
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<li><a href="https://www.bindingdb.org/rwd/bind/index.jsp">BindingDB</a>
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- A database of compounds and targes.</li>
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</ul></li>
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<li>Protein-Protein Interaction
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<ul>
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<li><a href="https://string-db.org/">STRING</a> - Protein-Protein
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Interaction Networks for several organisms.</li>
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<li><a href="https://thebiogrid.org/">BioGRID</a> - Database of Protein,
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Genetic and Chemical Interactions.</li>
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<li><a
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href="http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/">HIPPIE</a> -
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Human Protein-Protein Interaction database.</li>
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</ul></li>
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</ul>
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<h2 id="preprocess">Preprocess</h2>
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<ul>
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<li><a href="https://github.com/cdk/cdk">Chemistry Development Kit</a> -
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A software of cheminformatics and Machine Learning.</li>
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<li><a href="https://github.com/rdkit/rdkit">RDKit</a> - A software of
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cheminformatics and Machine Learning.</li>
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<li><a href="https://scanpy.readthedocs.io/en/stable/">Scanpy</a> -
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scRNA analysis library in Python.</li>
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<li><a href="https://satijalab.org/seurat/">Seurat</a> - scRNA analysis
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library in R.</li>
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</ul>
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<h2 id="machine-learning-tasks-and-models">Machine Learning Tasks and
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Models</h2>
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<h3 id="drug-repurposing">Drug Repurposing</h3>
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<ul>
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<li><a
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href="https://github.com/kexinhuang12345/DeepPurpose">DeepPurpose</a> -
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A DL Library for Drug Repurposing and so on.</li>
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<li><a href="https://github.com/gnn4dr/DRKG">DRKG</a> - A library for
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biological knowledge graph.</li>
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</ul>
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<h3 id="drug-target-interaction">Drug Target Interaction</h3>
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<ul>
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<li><a href="https://github.com/FangpingWan/NeoDTI">NeoDTI</a> - A
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library for Drug Target Interaction.</li>
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</ul>
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<h3 id="compound-protein-interaction">Compound Protein Interaction</h3>
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<ul>
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<li><a
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href="https://github.com/mhlee0903/multi_channels_PINN">MCPINN</a> - A
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library for drug discovery using Compound Protein Interaction and
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Machine Learning.</li>
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<li><a
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href="https://github.com/lifanchen-simm/transformerCPI">TransformerCPI</a>
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- A library for Compound Protein Interaction prediction using
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Transformer.</li>
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</ul>
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<h3 id="pre-trained-embedding">Pre-trained embedding</h3>
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<ul>
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<li><a href="https://github.com/facebookresearch/esm">Evolutionary Scale
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Modeling</a> - a library for protein embeddings.</li>
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<li><a
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href="https://github.com/seyonechithrananda/bert-loves-chemistry">ChemBERTa-2</a>
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- a library for chemical embeddingg and prediction.</li>
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</ul>
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<h3 id="llm-for-biology">LLM for biology</h3>
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<ul>
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<li><a
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href="https://huggingface.co/AI4Chem/ChemLLM-7B-Chat">AI4Chem/ChemLLM-7B-Chat</a>
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- LLM for chemical and molecule science</li>
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<li><a href="https://github.com/microsoft/BioGPT">BioGPT</a> - LLM for
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Biomedical text generation</li>
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</ul>
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