jaeswift-website/api/data/awesomelist/inoue0426--awesome-computational-biology.json

{"slug": "inoue0426--awesome-computational-biology", "title": "Awesome Computational Biology", "description": "Awesome list of computational biology.", "github_url": "https://github.com/inoue0426/awesome-computational-biology", "stars": "122", "tag": "Miscellaneous", "entry_count": 242, "subcategory_count": 13, "subcategories": [{"name": "Table of Contents", "parent": "", "entries": [{"name": "Awesome Computational Biology", "url": "#awesome-computational-biology-", "description": ""}]}, {"name": "scRNA", "parent": "Databases", "entries": [{"name": "CZ CELLxGENE", "url": "https://cellxgene.cziscience.com/", "description": "Single-cell dataset repository and interactive explorer from the Chan Zuckerberg Initiative."}, {"name": "Gene Expression Omnibus", "url": "https://www.ncbi.nlm.nih.gov/geo/", "description": "Public functional genomics database."}, {"name": "Human Cell Atlas", "url": "https://www.humancellatlas.org/", "description": "Open global atlas of all cells in the human body."}, {"name": "Single Cell PORTAL", "url": "https://singlecell.broadinstitute.org/single_cell", "description": "Public database for single-cell RNA."}, {"name": "Single Cell Expression Atlas", "url": "https://www.ebi.ac.uk/gxa/sc/home", "description": "Public database for single-cell RNA."}]}, {"name": "Compound", "parent": "Databases", "entries": [{"name": "PubChem", "url": "https://pubchem.ncbi.nlm.nih.gov/", "description": "One of the largest chemical databases (compounds, genes, and proteins)."}, {"name": "ChEBI", "url": "https://www.ebi.ac.uk/chebi/", "description": "Database focused on small chemical compounds."}, {"name": "ChEMBL", "url": "https://www.ebi.ac.uk/chembl/", "description": "Bioactive molecules with drug-like properties."}, {"name": "ChemSpider", "url": "http://www.chemspider.com/", "description": "Chemical structure database."}, {"name": "DrugTargetCommons", "url": "https://drugtargetcommons.fimm.fi/", "description": "Community platform for curating and 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"https://www.rcsb.org/", "description": "3D structures of proteins, nucleic acids, complexes."}, {"name": "UniProt", "url": "https://www.uniprot.org/", "description": "Functional information on proteins."}, {"name": "AlphaFold Protein Structure Database", "url": "https://alphafold.ebi.ac.uk/api-docs", "description": "3D protein structure predictions."}, {"name": "RCSB Protein Data Bank", "url": "https://www.rcsb.org/", "description": "Repository for structural data of biological molecules."}, {"name": "Critical Assessment of Structure Prediction (CASP)", "url": "https://predictioncenter.org/", "description": "Assessing methods for protein structure prediction."}, {"name": "Uniclust", "url": "https://uniclust.mmseqs.com/", "description": "Clustered protein sequence databases."}, {"name": "UniRef", "url": "https://www.uniprot.org/uniref/", "description": "Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds."}, {"name": "CATH database", 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{"name": "CellMiner Cross Database (CellMinerCDB)", "url": "https://discover.nci.nih.gov/cellminercdb/", "description": "Integrates multiple cancer cell line databases."}, {"name": "STITCH", "url": "http://stitch.embl.de/", "description": "Chemical-protein interactions."}, {"name": "BindingDB", "url": "https://www.bindingdb.org/rwd/bind/index.jsp", "description": "Compounds and target database."}, {"name": "Davis kinase inhibitors DB", "url": "http://staff.cs.utu.fi/~aijrinas/dti/", "description": "Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research."}, {"name": "Kinase Inhibitor Bioactivity Data (KIBA)", "url": "https://janeliascicomp.github.io/KIBA/", "description": "Integrated bioactivity scores for kinase inhibitors combining Ki, Kd, and IC50 measurements."}, {"name": "PDBBind", "url": "https://www.pdbbind-plus.org.cn/", "description": "Binding affinity data for biomolecular complexes."}, {"name": "STRING", "url": "https://string-db.org/", 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{"name": "BindingDB Curated Sets", "url": "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes", "description": "Curated binding affinity datasets for protein–ligand interaction benchmarking."}, {"name": "Cancer Therapeutics Response Portal (CTRP)", "url": "https://portals.broadinstitute.org/ctrp/", "description": "Drug sensitivity profiles across \\~900 cancer cell lines for >400 compounds."}, {"name": "ClinTox", "url": "https://tdcommons.ai/single_pred_tasks/tox/#clintox", "description": "Clinical toxicity dataset contrasting FDA-approved drugs with those that failed clinical trials due to toxicity."}, {"name": "CPTAC (Clinical Proteomic Tumor Analysis Consortium)", "url": "https://proteomics.cancer.gov/programs/cptac", "description": "Multi-omic proteogenomic datasets for multiple cancer types linking proteomics with genomics."}, {"name": "CrossDocked2020", "url": "https://arxiv.org/abs/2001.01037", "description": "Large-scale dataset for 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