Table 1.
An overview of computational databases, web servers, and tools useful for coronavirus research.
| Resources | URL | Release date | Key features | References |
|---|---|---|---|---|
| Detection of SARS-CoV-2 Coronavirus | ||||
| CoV2ID | http://covid.portugene.com/cgi-bin/COVid_home.cgi | 2020 | Repository of manually curated available oligonucleotides for SARS-CoV-2. CoV2ID has information on 52 oligonucleotides, 38 PCR primers, 14 probes, and 7 detection protocols to perform laboratory testing for SARS-CoV-2. | 45 |
| Resources for Host-Pathogen genome analysis | ||||
| CoVDB | http://covdb.microbiology.hku.hk | 2007 | Repository of known annotated coronavirus sequence with more than3000 records, belonging to various strains like coronavirus HKU1, SARS coronavirus belonging to bat, coronavirus HKU2 group 1 belonging to bat, coronaviruses 2c group coronaviruses group 2d, and 20 other coronaviruses strains. | 46 |
| DBatVir | http://www.mgc.ac.cn/DBatVir/ | 2014 | Repository of well-curated 4100 bat-associated viruses' genomes belonging to 23 viral families identified from 196 species of the bat across 69 countries. Presently, it contains 3873 sequences belonging to the coronaviridae family, of which 1393 are alphacoronavirus, 1181 betacoronavirus, and 1299 unclassified coronavirus. Further, DBatVir also provides details on the virus taxonomy lineage; host information such as sample type, collection date, and sampling country, and published data on the pathogenesis and epidemiology of several bat-associated emerging infectious diseases. | 47 |
| Genome Detective Typing Tool | www.genomedetective.com | 2020 | Web-based tool to identify and characterize the novel coronavirus genomes | 48 |
| MapMyCorona | http://shiny.mapmycorona.org/ | 2020 | MapMyCorona is an online tool using BLASTserver for identification of SARS CoV-2 sequences (protein or DNA) which finally displays the topmost hits in a well-organized spatial and temporal fashion. | |
| NCBI virus | https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/ | 2017 | A community web portal of sequences data of Virus with an integrative, value-added resource designed to support data retrieval, presentation, and investigation of various well-curated collection of sequences belonging to virus and datasets | 49 |
| Betacoronavirus BLAST | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=Betacoronavirus&LINK_LOC=blasttab | 2020 | Recently developed BLAST database focused on the SARS-CoV-2, containing betacoronavirus nucleotide sequence data from GenBank and RefSeq. | 50 |
| GISAID | https://www.gisaid.org/ | 2017 | Repository of sequence, clinical and epidemiological data belonging to influenza viruses and recently included SARS-CoV-2 | 51 |
| VADR | https://github.com/nawrockie/vadr | 2019 | Web-server validates and annotates sequences submitted to the GenBank | 52 |
| Docking servers for COVID-19 targets-ligand interactions | ||||
| COVID-19 Docking Server | http://ncov.schanglab.org.cn | 2020 | A powerful web server that helps in predicting the binding interaction affinity of COVID-19 targets and the probable ligands like peptide, antibody, and small molecules. | 53 |
| D3Targets-2019-nCoV | https://www.d3pharma.com/D3Targets-2019-nCoV/index.php | 2020 | An online server developed to recognize the potential targets for antivirals against SARS-CoV-2 through protein structure-based virtual screening. | 54 |
| Resources for Drug Discovery | ||||
| AVCpred | http://crdd.osdd.net/servers/avcpred | 2017 | Web server to predict and design potential antiviral compounds against deadly viruses. | 55 |
| AVPdb | http://crdd.osdd.net/servers/avpdb | 2014 | Database of comprehensive experimentally validated Antiviral peptides (AVPs) targeting more than 60 therapeutically medically important SARS coronaviruses. AVPdb database also contains information of numerous peptide-like anti-coronavirus peptides with detailed mechanisms of their mode of action against SARS-CoV-1 | 56 |
| AVPpred and AntiVPP 1.0 | http://crdd.osdd.net/servers/avppred | |||
| https://github.com/bio-coding/AntiVPP | 2012 | |||
| 2019 | Comprehensive virus-specific web-resources to explore potential sequences of the peptide having antiviral properties against SARS coronaviruses of human. | 57, 58 | ||
| ClinicalTrials.gov COVID-19 related studies | https://clinicaltrials.gov/ct2/results/details?cond=COVID-19 | ClinicalTrials.gov is a government website with an easy access option to publicly and privately supported human clinical studies information with an extensive collection of diseases and conditions. On May 7, 2020, information on 1254 clinical studies on COVID-19 are available | ||
| Resources for vaccine discovery | ||||
| CoronaVIR | https://webs.iiitd.edu.in/raghava/coronavir/ | 2020 | CoronaVIR: a multi-omics repository of SARS-CoV-2 coronaviruses with detailed information on genomic, proteomic, diagnostic, and therapeutic knowledge to fight against the pandemic disease. | 59 |
| IEDB | www.iedb.org | 2019 | A free resource for searching and exploring experimentally validated T cell epitope and antibody -information about infectious disease, allergy, autoimmunity, and transplantation. Additionally, IEDB also provides several immunoinformatic tools for the prediction of putative epitopes from antigenic proteins, for further analysis of epitope data. | 60, 61 |
| ViPR | http://www.viprbrc.org | 2012 | ViPR is an NIAID-funded data repository and analysis tool for numerous human pathogenic viruses including the entire coronaviridae family. Recently, ViPR has developed the 2019 Novel Coronavirus (2019-nCoV) portal in ViPR to support research efforts on this emerging public health threat (https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov). This open-access resource is updated daily and provides the necessary analytical tools and genomic data for SARS-CoV-2 and related betacoronaviruses. | 62 |
| IRD | Influenza Research Database like the ViPR Resource is also an NIAID-funded project with a specific focus on viral research pathogens causing (re)emerging infectious diseases. IRD along with ViPR maintains and updates the novel coronavirus (2019-nCoV) portal hosted in ViPR | 63 | ||
| Visualization tools to map the coronavirus spread | ||||
| GLEaMviz | http://www.gleamviz.org/ | 2011 | User-friendly graphical interface to explore the spread of human-to-human infectious diseases and emerging scenarios at the global scale | 64 |
| EpiRisk | https://epirisk.net/ | 2020 | Web-based interface for investigating the risk of the coronavirus | |
| Nextstrain COVID-19 genetic epidemiology | https://nextstrain.org | 2020 | It is a real-time genetic tracking tool to map how the virus spread and pathogen evolution to further accelerate research on COVID-19 disease; Nextstrain is incorporating country-wise genomes information of SARS-CoV-2 epidemiology of novel coronavirus analyses and situation report. | |
| Phyloscanner | https://github.com/BDI-pathogens/phyloscanner | 2018 | Analyses pathogen genetic diversity and relationships between and within hosts at once, in windows along the genome. | 65 |
| Cloud Computing Unified Platforms | ||||
| ATRIO: A Composable Cloud | https://atrio.io/ | ATRIO is a computing platform to eliminate the challenges between user infrastructure and cloud computing. Atrio is presently offering its users free high-performance GPU and CPU computing resources and containerized toolsets to facilitate COVID-19 research. | ||
| ELIXIR | https://elixir-europe.org/ | A group of Intergovernmental organizations working together to curate all resources of life science across Europe. Currently, ELIXIR's extends its services to support SARS-CoV-2 research by ensuring the exponential increasing genomic data, resources, and scientific publications on SARS-CoV-2 to be freely accessible to all across worldwide. | ||