Table 2.
Curated list of COVID-19-specific resources and repositories relevant to computational drug repurposing.
| Resource/ data type | Resource name | Website | Description | Reference | |
|---|---|---|---|---|---|
| COVID-19 platform | CORD-19 | https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge | Scholarly articles on COVID-19, SARS-CoV-2, and other related coronaviruses, with a focus on natural language processing and other AI techniques | 97 | |
| COVID-19 portfolio | https://icite.od.nih.gov/covid19/search/ | Publications and preprints on COVID-19 and SARS-CoV-2 | – | ||
| COVIDScholar | https://covidscholar.org/ | Search engine that utilizes natural language processing to aid in the search for COVID-19 articles | – | ||
| COVID-19 research explorer | https://covid19-research-explorer.appspot.com/ | Search engine for COVID-19 that operates on question-based searches | – | ||
| SPIKE-CORD | https://spike.covid-19.apps.allenai.org/search/covid19 | Search engine for CORD-19 which operates on query modes to perform extractive searches | – | ||
| Virus-CKB | https://www.cbligand.org/g/virus-ckb | Knowledgebase for research on COVID-19 and similar viral infections | 123 | ||
| SciSight | https://scisight.apps.allenai.org/ | Tool used to visualize the directions of the emerging literature network related to COVID-19 | – | ||
| KnetMiner | https://knetminer.org/COVID-19/ | Search engine that aids in COVID-19 related search queries based on keywords, gene lists, and genomic regions | – | ||
| COVID-19 Primer | https://covid19primer.com/dashboard | Tool that uses natural language processing (NLP) to summarize research trends, news coverage, and social media discussions on the topic of COVID-19 and SARS-CoV-2 | – | ||
| COVID-19 drug and gene set library | https://maayanlab.cloud/covid19/ | A collection of drug and gene sets related to COVID-19 research contributed by the community | 35 | ||
| CDC COVID-19 Databases and Journals | https://www.cdc.gov/library/researchguides/2019novelcoronavirus/databasesjournals.html | Compilation of selected databases and journals that can help researchers to find scholarly articles and data relating to COVID-19 | – | ||
| LitCovid | https://www.ncbi.nlm.nih.gov/research/coronavirus/ | A curated literature hub for tracking up-to-date scientific information about SARS-CoV-2 | 124 | ||
| iSearch COVID-19 portfolio | https://icite.od.nih.gov/covid19/search/ | An expert-curated database containing published papers and preprints | – | ||
| WHO COVID-19 research article database | https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov | A database gathering the latest international multilingual scientific findings and knowledge on COVID-19 | – | ||
| COVID-KOP | https://covidkop.renci.org/ | Biomedical reasoning system for data collected about the COVID-19 pandemic, including information on drugs, literature co-occurrences and phenotypes | 125 | ||
| HIT-COVID | https://akuko.io/post/covid-intervention-tracking | Quantification of the effectiveness of public health measures on SARS-CoV-2 transmission | 126 | ||
| COVID Moonshot | https://covid.postera.ai/covid | Crowdsourced initiative to accelerate the development of a COVID-19 antiviral | 127 | ||
| CIDO | http://www.ontobee.org/ontology/CIDO | Community-based ontology that supports COVID-19 knowledge and data standardization, integration, sharing, and analysis | 128 | ||
| COVEX | https://exbio.wzw.tum.de/covex/about | Online network and systems medicine platform for data analysis that integrates virus–human interactions for SARS-CoV-2 and SARS-CoV-1 | 129 | ||
| The COVIDome Project | https://www.ncbi.nlm.nih.gov/sars-cov-2/ | Collaborative effort to generate multidimensional datasets from biospecimens from COVID-19 patients and controls | – | ||
| NCBI SARS-CoV-2 Resource | https://www.ncbi.nlm.nih.gov/sars-cov-2/ | An expert-curated database which was developed to increase the useability of existing resources | – | ||
| PDBe COVID-19 | https://www.ebi.ac.uk/pdbe/covid-19 | 3D-structure data for large biological molecules, such as proteins and nucleic acids, that are specific to SARS-CoV-2 | 130 | ||
| Compound database | ZINC15 | https://zinc15.docking.org/ | 3D formats of purchasable compounds and their different properties, such as rings, substances, tranches, and patterns | 45 | |
| Drug response | PharmGKB | https://www.pharmgkb.org/ | Data on the impact of genetic variations on drug response and annotated information on drugs | 131 | |
| Drugs and drug targets | IUPHAR/BPS guide to pharmacology | https://www.guidetopharmacology.org/ | Information on drug targets, and on prescription and experimental medications that act on them | – | |
| DrugBank | https://www.drugbank.ca/ | Information on drugs and their chemical and pharmacological properties; this resource also contains information on drug targets and their sequences, structures, and pathways | 132 | ||
| Drug Target Commons Database | https://drugtargetcommons.fimm.fi/ | Bioactivity data for drugs and their targets | 84 | ||
| Drugs | Drug repurposing for COVID-19 | http://covid19.md.biu.ac.il/ | Database of existing drugs that have potential or proven efficacy against SARS-CoV-2 | – | |
| Binding affinities | BindingDB | https://www.bindingdb.org/bind/index.jsp | Information on the binding affinities between molecular entities and protein targets | 83 | |
| Gene | GenBank | https://www.ncbi.nlm.nih.gov/genbank/ | Publicly available DNA sequences | 133 | |
| EMBL-ENA | https://www.ebi.ac.uk/ena | Nucleotide sequencing information | 134 | ||
| GeneCards | https://www.genecards.org/ | Annotated and predicted human genes | 135 | ||
| CMAP | https://www.broadinstitute.org/connectivity-map-cmap | Gene expression profiles and disease-associated genes | 136 | ||
| MSigDB | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp | Annotated gene sets that can be utilized with Gene Set Enrichment Analysis (GSEA) software | 137 | ||
| Protein | UniProt | https://covid-19.uniprot.org/uniprotkb?query=* | Information on protein sequence and annotation of SARS-CoV-2 | 138 | |
| Swiss-Prot | https://www.uniprot.org/statistics/Swiss-Prot | Part of UniProt, this resource includes protein sequences and their functional information | 139 | ||
| PDB | https://www.rcsb.org/ | 3D structure data for large biological molecules, such as proteins and nucleic acids | 130 | ||
| PRIDE | https://www.ebi.ac.uk/pride/ | Mass spectrometry proteomics and genomic data | 140 | ||
| CORUM | http://mips.helmholtz-muenchen.de/corum/ | Protein complexes, protein subunits, literature references, and experimental reports | 141 | ||
| Multi type | KEGG | https://www.genome.jp/kegg | Information on drugs, genes, proteins and pathways | 142 |