Foldingathome COVID-19 Datasets

Tutorials

• Folding@home COVID-19 efforts by Folding@home Consortium
  

Tools & Applications

• SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2 (953.7 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 COVID Moonshot absolute free energy calculations by The Voelz lab at Temple University
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) dimer simulations: A 2.9 ms dataset of the SARS-CoV-2 main viral protease (apo, dimer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 2.6 ms equilibrium dataset of the SARS-CoV-2 main viral protease (apo, monomer) by The Chodera lab at MSKCC
  
• SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 6.4 ms dataset of the SARS-CoV-2 main viral protease (apo, monomer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp10 dataset: A 6.1 ms dataset of the SARS-CoV-2 nsp10 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 macrodomain dataset: An 11 ms dataset of the SARS-CoV-2 nsp3 macrodomain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp3 pl2pro domain dataset: An 731 µs dataset of the SARS-CoV-2 nsp3 pl2pro domain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp7 simulations: A 3.7 ms dataset of the SARS-CoV-2 nsp7 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp8 simulations: A 1.8 ms dataset of the SARS-CoV-2 nsp8 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 nsp9 simulations: A 9 ms dataset of the SARS-CoV-2 nsp9 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 RNA polymerase (nsp12, RdRP) dataset: A 3.4 ms dataset of the SARS-CoV-2 nsp12 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike protein dataset: A 1.2 ms dataset of the SARS-CoV-2 spike protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
  
• SARS-CoV-2 spike RBD (with glycosylation) (1.8 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD (without glycosylation) (1.9 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to human ACE2 receptor (173.8 us): Wild-type and mutant simulations by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97 (623.7 us) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S309 (1.1 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309 (907.0 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309 (923.2 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  

Publications

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity by Emma C. Thomson, Laura E, Rosen, James G. Shepherd, et al.
  
• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape by Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, et al.
  
• SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome by Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, View ORCID ProfileRafal P. Wiewiora, Matthew F. D. Hurley, Aoife M Harbison, Carl A Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman
  

PubSeq - Public Sequence Resource

Tutorials

• PubSeq Documentation by PubSeq development team
  
• PubSeq FAQ by PubSeq development team
  
• Query metadata by PubSeq development team
  
• REST API by PubSeq development team
  
• Submitting a sequence by PubSeq development team
  

Tools & Applications

• Source code for (meta)data uploader by PubSeq development team
  
• Source code for CWL workflows by PubSeq development team
  
• Source code for website by PubSeq development team
  

Publications

• Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.
  

Serratus: Ultra-deep Search for Novel Viruses - Versioned Data Release

Tools & Applications

• Serratus Explorer by Serratus Team
  
• Tantalus: An R Package for exploration of Serratus data by Serratus Team
  

Publications

• coronaSPAdes. From biosynthetic gene clusters to RNA viral assemblies by Meleshko D., Hajirasouliha I., and Korobeynikov A. (2021)
  
• Diversification of mammalian deltaviruses by host shifting by Bergner L.M., Orton R.J., et al (2021)
  
• Petabase-scale sequence alignment catalyses viral discovery by Edgar R., Taylor J., Lin V., et al (2021)
  
• Ribovirus classification by a polymerase barcode sequence by Babaian A., and Edgar R. (2021)
  

Protein Data Bank 3D Structural Biology Data

Tutorials

• File Download Services by RCSB PDB
  
• Get to Know a Dataset: Protein Data Bank 3D Structural Biology Data by RCSB PDB
  
• PDB 101 by RCSB PDB
  

Publications

• Announcing the worldwide Protein Data Bank by Berman, H., Henrick, K. & Nakamura, H.
  
• Protein Data Bank: the single global archive for 3D macromolecular structure data by wwPDB consortium
  

COVID-19 Harmonized Data

Tutorials

• How Talend is joining the fight against COVID-19 by Thomas Bennett
  

Tools & Applications

• Stitch COVID-19 Integration by Jeff Huth
  
• Tap COVID-19 Python by Jeff Huth
  

STOIC2021 Training

Tools & Applications

• STOIC2021 Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Publications

• How Well Do Self-Supervised Models Transfer to Medical Imaging? by Anton J, Castelli L, Chan MF, Outthers M, Tang WH, Cheung V, et al.
  
• Study of Thoracic CT in COVID-19: The STOIC Project by Revel MP, Boussouar S, de Margerie-Mellon C, Saab I, Lapotre T, Mompoint D, et al.
  

COVID-19 Data Lake

Tutorials

• A public data lake for analysis of COVID-19 data by AWS Data Lake Team
  AWS GlueAmazon AthenaAmazon ComprehendAmazon KendraAmazon QuickSight
• Exploring the public AWS COVID-19 data lake by AWS Data Lake Team
  Amazon AthenaAWS GlueAmazon SageMaker
• How to use SQL to query data in S3 Bucket with Amazon Athena and AWS SDK for .NET by AWS ProServe US West Applications Team
  Amazon AthenaAWS GlueAmazon S3AWS CloudFormation

Tools & Applications

• CloudFormation template for Glue Catalog table definitions by AWS Data Lake Team
  
• Explore the COVID-19 data lake public S3 bucket by AWS Data Lake Team
  

Covid Job Impacts - US Hiring Data Since March 1 2020

Tutorials

• Documentation of dataset schemas by Greenwich.HR
  

Tools & Applications

• CovidJobImpats.Greenwich.HR - online visualization of daily hiring data and weekly unemployment data including links to recorded discussions using the data by Greenwich.HR and OneModel Inc.
  

DNAStack COVID19 SRA Data

Tutorials

• Viral lineage assignment by Heather Ward
  AWS BatchAmazon EC2Amazon S3

Tools & Applications

• Viral AI by DNAstack
  

REDASA COVID-19 Open Data

Tools & Applications

• Curadr - Curation Platform by REDASA Consortium, Imperial College London
  

Publications

• Using a Secure, Continually Updating, Web Source Processing Pipeline to Support the Real-Time Data Synthesis and Analysis of Scientific Literature: Development and Validation Study by Uddhav Vaghela, Simon Rabinowicz, Paris Bratsos, Guy Martin, Epameinondas Fritzilas, et al.
  

COVID-19 Genome Sequence Dataset

Tools & Applications

• Download SRA sequence data using Amazon Web Services (AWS) by NCBI SRA
  

COVID-19 Open Research Dataset (CORD-19)

Tools & Applications

• COVID-19 Open Research Dataset Challenge (CORD-19) by Kaggle