update lists
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@@ -22,11 +22,15 @@ href="https://en.wikipedia.org/wiki/Computational_biology">Wikipedia</a></p>
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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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<li><a href="#clinical-trial">Clinical Trial</a></li>
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</ul></li>
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<li><a href="#api">API</a></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-response-prediction">Drug Response
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Prediction</a></li>
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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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@@ -61,7 +65,20 @@ 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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drug, moa, target etc.</li>
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<li><a href="https://idrblab.net/ttd/full-data-download">Therapeutic
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Target Database</a> - collections of drug-target, target-disease, and
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drug-disease dataset.</li>
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<li><a href="https://zinc.docking.org/">ZINC ligand discovery
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database</a> - Free database of commercially-available compounds for
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virtual screening.</li>
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<li><a href="http://moleculenet.ai/">MoleculeNet</a> - Benchmark for
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molecular machine learning.</li>
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<li><a
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href="https://www.sciencedirect.com/science/article/abs/pii/S0166354220302412">Ames
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Mutagenicity dataset</a> - Dataset for predicting mutagenicity.</li>
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<li><a href="https://www.antibody-drug.com/">ADCdb</a> - Database for
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antibody-drug conjugates. ### 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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@@ -81,8 +98,16 @@ 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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Structure Database</a> - Database of 3D protein structures.</li>
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<li><a href="https://www.rcsb.org/">RCSB Protein Data Bank (PDB)</a> -
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Repository of 3D structural data of large biological molecules.</li>
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<li><a href="https://predictioncenter.org/">Critical Assessment of
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Structure Prediction (CASP)</a> - Experiment for advancing the methods
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of predicting protein structure from sequence.</li>
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<li><a href="https://uniclust.mmseqs.com/">Uniclust</a> - Collection of
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clustered protein sequence databases.</li>
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<li><a href="https://www.cathdb.info/">CATH database</a> - Hierarchical
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classification of protein domain structures. ### 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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@@ -92,8 +117,23 @@ 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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Cancer Genomics. This has overall metaview for a lot of patients.</li>
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<li><a href="https://www.10xgenomics.com/resources/datasets">10x
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Genomics Dataset</a> - Collection of single-cell datasets.</li>
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<li><a href="https://gtexportal.org/home/">The Genotype-Tissue
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Expression (GTEx)</a> - Resource for studying human gene expression and
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regulation.</li>
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<li><a href="https://depmap.org/portal/">Dependency Map (DepMap)</a> -
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Genome-wide CRISPR-Cas9 screens in cancer cell lines.</li>
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<li><a href="https://cancer.sanger.ac.uk/cosmic">Catalogue Of Somatic
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Mutations In Cancer (COSMIC)</a> - Comprehensive resource for exploring
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somatic mutations in human cancers.</li>
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<li><a href="https://www.ebi.ac.uk/metagenomics/">MGnify</a> - Free
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resource for archiving, analysis, and browsing of metagenomic and
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metatranscriptomic data.</li>
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<li><a href="http://jaspar.genereg.net/">JASPAR</a> - Open-access
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database of curated, non-redundant transcription factor binding
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profiles. ### 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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@@ -110,8 +150,6 @@ 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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@@ -127,6 +165,9 @@ 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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<li><a href="https://discover.nci.nih.gov/cellminercdb/">CellMiner Cross
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Database (CellMinerCDB)</a> - Integration of multiple cancer cell line
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databases.</li>
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</ul></li>
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<li>Chemical Protein Interaction
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<ul>
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@@ -134,6 +175,12 @@ lines.</li>
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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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<li><a href="http://www.pdbbind.org.cn/">PDBBind</a> - Database of
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experimentally measured binding affinity data for biomolecular
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complexes.</li>
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<li><a href="https://arxiv.org/abs/2001.01037">CrossDocked2020</a> -
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Large-scale dataset for machine learning in structure-based virtual
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screening.</li>
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</ul></li>
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<li>Protein-Protein Interaction
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<ul>
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@@ -145,6 +192,29 @@ Genetic and Chemical Interactions.</li>
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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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<li>Knowledge Graph
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<ul>
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<li><a href="https://github.com/SuLab/DrugMechDB/tree/2.0.1">Drug
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Mechanism Database (DrugMechDB)</a>: database of the mechanism of action
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from a drug to a disease.</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. ### Clinical Trial</li>
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</ul></li>
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<li><a href="https://clinicaltrials.gov/">ClinicalTrials.gov</a> -
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Database of privately and publicly funded clinical studies.</li>
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<li><a href="https://icd.who.int/browse10/2019/en">ICD10</a> -
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International Classification of Diseases, 10th revision.</li>
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<li><a href="https://eudract.ema.europa.eu/">EU Drug Regulating
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Authorities Clinical Trials DB (EudraCT)</a> - European database of
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clinical trials.</li>
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<li><a href="https://mimic.mit.edu/">MIMIC-IV</a> - Freely accessible
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critical care database.</li>
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</ul>
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<h2 id="api">API</h2>
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<ul>
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<li><a
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href="https://www.nlm.nih.gov/dataguide/edirect/esearch.html">PubMed
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esearch</a>: API for searching articles in PubMed.</li>
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</ul>
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<h2 id="preprocess">Preprocess</h2>
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<ul>
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@@ -159,13 +229,26 @@ 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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<h2 id="drug-response-prediction">Drug Response Prediction</h2>
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<ul>
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<li><a href="https://github.com/inoue0426/drGAT">drGAT</a>: A model for
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drug response prediction with gene explainability with attention
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mechanism.</li>
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<li><a href="https://github.com/weiba/MOFGCN/tree/main">MOFGCN</a>: GCN
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+ heterogeneous network</li>
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<li><a
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href="https://ieeexplore-ieee-org.ezp2.lib.umn.edu/stamp/stamp.jsp?tp=&arnumber=8723620&tag=1">DeepDSC</a>:
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Autoencoder + Fully Connected NN</li>
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<li><a href="https://github.com/minwoopak/heteronet">DGDRP</a>:
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Multi-view embedding NN.</li>
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<li><a href="https://github.com/zhejiangzhuque/DeepAEG">DeepAEG</a>: GNN
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Embedding + Attention</li>
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</ul>
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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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A DL Library for Drug Repurposing.</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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@@ -198,4 +281,14 @@ 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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<li><a href="https://github.com/ncbi/GeneGPT">GeneGPT</a> - LLM for
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biomedical information with several API.</li>
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<li><a href="https://github.com/yiqunchen/GenePT">GenePT</a> -
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foundation LLM for single cell data</li>
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<li><a href="https://github.com/cantinilab/scPRINT">scPRINT</a> -
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scPRINT is pretrained on 50M cells to denoise and perform zero
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imputation of any single cell RNAseq profile.</li>
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</ul>
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<p><a
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href="https://github.com/inoue0426/awesome-computational-biology">computationalbiology.md
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Github</a></p>
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