COVID-19 RESOURCES

This page provides a selection of COVID-19 links related to epitope prediction and analysis. We perform regular checks for broken links, but please let us know if any links are broken or in need of updating. Likewise, we would love to hear of any additions that you feel should be included in our list of selected links.

ANTIBODIES & VACCINES

• Anti-SARS-CoV-2 Monoclonal Antibodies - COVID-19 therapeutic monoclonal antibody candidates, research and trials (COVID-19 Real-Time-Learning Network, CDC-IDSA).
• CoronaVIR: Computational Resources on Novel Coronavirus - Mapping of Experimentally Validated Epitopes (Bioinformatics Centre, Institute of Microbial Technology, India).
• COVIC-DB - Potency, efficacy and structural analysis of SARS-Cov-2 antibodies (Coronavirus Immunotherapy Consortium (CoVIC), La Jolla Institute for Immunology).
• DBCOVP: Database of Coronavirus Virulent glycoProteins - Resource for exploring the functional and immunological properties of coronavirus virulent glycoproteins for vaccine target discovery (CSIR-IMMT, Bhubaneswar, India).
• Information for Laboratories about Coronavirus (COVID-19) from the CDC.
• NCBI SARS-CoV-2 Resources - COVID-19 clinical resources related to vaccines and therapeutic antibodies.
• SARS-CoV-2 Immune Epitope Search - A resource hosted by the Virus Pathogen Resource (ViPR; U.S. National Institute of Allergy and Infectious Diseases, NIH).
• Target and Drug Data for Coronavirus in the Therapeutic Target Database (TTD) - a searchable database of anti-coronavirus agents, including monoclonal antibodies, protein/peptide drugs and vaccines (Bioinformatics and Drug Design Group, National University of Singapore).
• The Coronavirus Antibody Database (Cov-AbDab) - A database of coronavirus-binding antibody and nanobody sequences and structures (Oxford Protein Informatics Group).
• Vaccines & Immunity - COVID-19 vaccine candidates, research and trials (COVID-19 Real-Time-Learning Network, CDC-IDSA).

LITERATURE

• CDC Publications about COVID-19 for Laboratories.
• Cell Press Coronavirus Resource Hub.
• Elsevier Connect Novel Coronavirus Information Center.
• Frontiers Coronavirus Knowledge Hub.
• LitCovid - A curated and daily updated coronavirus literature hub for tracking up-to-date scientific information (NIH-NLM).
• New England Journal of Medicine Covid-19 Vaccine Resource Centre.
• Science journal's coronavirus resource.
• Springer Nature coronavirus (covid-19) resource.
• The British Medical Journal's Coronavirus (covid-19) Hub.
• The Lancet COVID-19 Resource Centre.
• Wiley Online Covid-19 Resource.

PORTALS

• COMBATdb - Oxford COvid-19 Multi-omic Blood ATlas database, generated by the COMBAT Consortium and hosted by the University of Oxford.
• COVID-19 Data Portal - Resource hosted by EMBL-EBI.
• COVID-19 Datasets - Datasets available at the Registry of Open Data on Amazon Web Services (AWS).
• COVID-19 UniProtKB -  Provides the latest available pre-release UniProtKB data for the SARS-CoV-2 coronavirus and other entries relating to the COVID-19 outbreak (UniProt).
• NCBI SARS-CoV-2 Resources (NIH-NLM).
• Open-Access Data and Computational Resources to Address COVID-19 from the NIH.
• SARS-CoV-2 - A resource hosted by the Virus Pathogen Resource (ViPR; U.S. National Institute of Allergy and Infectious Diseases, NIH).
• ViralZone Coronavirus Resource (Expasy, Swiss Institute of Bioinformatics (SIB)).
• WHO Coronavirus (COVID-19) Dashboard.

SEQUENCES

• Coronapp - A web app to discover and annotate and monitor mutations present in SARS-CoV-2 genomes, including partial sequences (Department of Pharmacy and Biotechnology, University of Bologna).
• CoVariants - A resource overview of SARS-CoV-2 variants and mutations of interest, enabled by data from GISAID (Institute of Social and Preventive Medicine, University of Bern, and Swiss Institute of Bioinformatics (SIB)).
• CoV-GLUE - Web application for the analysis of SARS-CoV-2 genome sequences (MRC-University of Glasgow Centre for Virus Research).
• CoVsurver - Mutation analysis of hCoV-19 at the GISAID.
• GISAID - Global initiative promoting rapid data sharing from the coronavirus causing COVID-19 and all influenza viruses. A global standard whole genome sequence database.
• NCBI SARS-CoV-2 Sequence Resources - Curated gene and protein sequence databases (NIH-NLM).
• Nextstrain - SARS-CoV-2 sequence resources.
• SARS-CoV-2 Database - A curated knowledge database for SARS-CoV-2 virus research (Center for Bioinformatics, UiT The Arctic University of Norway).
• SARS-CoV-2 variants in the EU/EEA - (European Centre for Disease Prevention and Control (ECDC)).

STRUCTURES

• AlphaFold computational predictions of COVID-19 protein structures - Open source resource of AlphaFold protein structure predictions (DeepMind).
• Coronavirus3D - 3D visualization and analysis of the SARS-CoV-2 (COVID-19) protein structures with respect to mutational patterns.
• Coronavirus 3D Structure Database (CoV3D) - A weekly updated resource for structures of coronavirus proteins and their recognition by antibodies and other molecules.
• CoVal - A repository of amino acid replacement mutations identified in the SARS-CoV-2 genome sequences, mapped onto their cryo-EM derived protein structures.
• COVID-19 Docking Server - A web server for docking small molecule, peptide or antibody to COVID-19 protein targets (Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology).
• COVID-19 Molecular Structure and Therapeutics Hub - A community-driven data repository and curation service for SARS-CoV-2 molecular structures, models, therapeutics, and simulations.
• DINC-COVID - A web server to incrementally dock ligands to COVID-19 related proteins (Physical and Biological Computing Group, Rice University, Texas).
• DockThor - Web server for protein-ligand docking providing covid-19 therapeutic target proteins and variants ready prepared for docking (GMMSB research group, National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil).
• I-TASSER modelling of SARS-CoV-2 structures (Zhang Lab, University of Michigan).
• PDB COVID-19/SARS-CoV-2 Resources (RCSB PDB).
• PDBe-KB COVID-19 Data Portal - Brings together all available PDB data from SARS-CoV-2 structures (EMBL-EBI).
• SWISS-MODEL SARS-CoV-2 Repository - database of annotated 3D protein structure homology models generated by the SWISS-MODEL homology-modelling pipeline (Swiss Institute of Bioinformatics (SIB).