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foldingathome-covid19.yaml
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foldingathome-covid19.yaml
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Name: Foldingathome COVID-19 Datasets
Description: >
[Folding@home](http://foldingathome.org) is a massively distributed computing
project that uses biomolecular simulations to investigate the [molecular origins of disease](https://foldingathome.org/diseases/)
and accelerate the discovery of new therapies. Run by the
[Folding@home Consortium](https://foldingathome.org/about/the-foldinghome-consortium/),
a worldwide network of research laboratories focusing on a variety of different
diseases, Folding@home seeks to address problems in human health on a scale
that is infeasible by another other means, sharing the results of these large-scale
studies with the research community through [peer-reviewed publications](https://foldingathome.org/papers-results/)
and publicly shared datasets.
During the [COVID-19 epidemic](https://en.wikipedia.org/wiki/Coronavirus_disease_2019),
Folding@home focused its resources on understanding the vulernabilities in
[SARS-CoV-2](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2),
the virus that causes COVID-19 disease, and working closely with a number of
experimental collaborators to accelerate progress toward effective therapies for
treating COVID-19 and ending the pandemic. In the process, it created the world's first
[exascale distributed computing resource](https://doi.org/10.1101/2020.06.27.175430),
enabling it to generate valuable scientific datasets of unprecedented size.
More information about Folding@home's COVID-19 research activities at the
[Folding@home COVID-19 page](https://foldingathome.org/diseases/infectious-diseases/covid-19/).
In addition to working directly with experimental collaborators and rapidly sharing
new research findings through preprint servers, Folding@home has joined other
researchers in committing to [rapidly share all COVID-19 research data](https://doi.org/10.1021/acs.jcim.0c00319),
and has joined forces with [AWS](https://aws.amazon.com/) and the
[Molecular Sciences Software Institute (MolSSI)](http://molssi.org) to share datasets of unprecented side
through the [AWS Open Data Registry](https://registry.opendata.aws/),
indexing these massive datsets via the [MolSSI COVID-19 Molecular Structure and Therapeutics Hub](https://covid.molssi.org/).
The complete index of all Folding@home datasets can be found [here](https://covid.molssi.org//org-contributions/#folding--home).
This repository contains several major datasets from this effort and comprises
the single largest collection of molecular simulation data ever released.
Documentation: https://github.com/FoldingAtHome/coronavirus
Contact: "[Folding@home](https://foldingathome.org/contact-us/)"
ManagedBy: "Folding@home"
UpdateFrequency: Datasets will be updated periodically as additional simulations are completed.
Tags:
- alchemical free energy calculations
- aws-pds
- biomolecular modeling
- coronavirus
- COVID-19
- foldingathome
- health
- life sciences
- molecular dynamics
- protein
- SARS-CoV-2
- simulations
- structural biology
License: "[CC0](https://creativecommons.org/share-your-work/public-domain/cc0/)"
Resources:
- Description: Simulations of SARS-CoV-2 and associated host proteins, with emphasis on discovering druggable cryptic pockets, documented at the [MolSSI COVID Hub](https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-protein-spike-spike-binding).
ARN: arn:aws:s3:::fah-public-data-covid19-cryptic-pockets
Region: us-east-2
Type: S3 Bucket
- Description: Simulations of SARS-CoV-2 and associated host proteins relevant to neutralization by therapeutic antibodies, documented at the [MolSSI COVID Hub](https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-bound-to-human-ace2).
ARN: arn:aws:s3:::fah-public-data-covid19-antibodies
Region: us-east-2
Type: S3 Bucket
- Description: Absolute free energy calculations of small molecules from the [COVID Moonshot](http://postera.ai), documented at the [MolSSI COVID Hub](https://covid.molssi.org//simulations/#foldinghome-expanded-ensemble-absolute-free-energy-calculations-of-potential-small-molecule-inhibitors-of-the-sars-cov-2-main-protease-from-the-covid-moonshot-3clpro-3clpro-protease-activity)
ARN: arn:aws:s3:::fah-public-data-covid19-absolute-free-energy
Region: us-east-2
Type: S3 Bucket
- Description: Simulations of target proteins and bound small molecules from the [COVID Moonshot](http://postera.ai), documented at the [MolSSI COVID Hub](https://covid.molssi.org//simulations/#foldinghome-sars-cov-2-main-protease-apo-monomer-simulations-3clpro-3clpro-protease-activity)
ARN: arn:aws:s3:::fah-public-data-covid19-moonshot-dynamics
Region: us-east-2
Type: S3 Bucket
DataAtWork:
Tools & Applications:
- Title: "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)"
URL: https://covid.molssi.org//simulations/#foldinghome-sars-cov-2-main-protease-apo-monomer-simulations-3clpro-3clpro-protease-activity
AuthorName: "The Chodera lab at MSKCC"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 COVID Moonshot absolute free energy calculations"
URL: https://covid.molssi.org//simulations/#foldinghome-expanded-ensemble-absolute-free-energy-calculations-of-potential-small-molecule-inhibitors-of-the-sars-cov-2-main-protease-from-the-covid-moonshot-3clpro-3clpro-protease-activity
AuthorName: "The Voelz lab at Temple University"
AuthorURL: http://www.voelzlab.org/
- Title: "SARS-CoV-2 spike protein dataset: A 1.2 ms dataset of the SARS-CoV-2 spike protein in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-protein-spike-spike-binding
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp10 dataset: A 6.1 ms dataset of the SARS-CoV-2 nsp10 protein in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp10-nsp10-nil
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "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"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp12-rdrp-nil
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp3 macrodomain dataset: An 11 ms dataset of the SARS-CoV-2 nsp3 macrodomain in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp3-macrodomain-macrodomain-host-immune-response
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp3 pl2pro domain dataset: An 731 µs dataset of the SARS-CoV-2 nsp3 pl2pro domain in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp3-pl2pro-domain-plpro-plpro-protease-activity
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "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"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp5-3clpro-3clpro-protease-activity
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "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"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp5-3clpro-3clpro-protease-activity
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp7 simulations: A 3.7 ms dataset of the SARS-CoV-2 nsp7 protein in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp7-nsp7-nil
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp8 simulations: A 1.8 ms dataset of the SARS-CoV-2 nsp8 protein in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp8-nsp8-nil
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 nsp9 simulations: A 9 ms dataset of the SARS-CoV-2 nsp9 protein in search of cryptic pockets"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-nsp9-nsp9-nil
AuthorName: "The Bowman lab at Washington University in St. Louis"
AuthorURL: https://bowmanlab.biochem.wustl.edu
- Title: "SARS-CoV-2 spike RBD bound to human ACE2 receptor (173.8 us): Wild-type and mutant simulations"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-bound-to-human-ace2
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD bound to monoclonal antibody S309 (1.1 ms)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-bound-to-monoclonal-antibody-s309
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309 (923.2 µs)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-with-p337l-mutation-bound-to-monoclonal-antibody-s309
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309 (907.0 µs)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-with-p337a-mutation-bound-to-monoclonal-antibody-s309
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97 (623.7 us)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-bound-to-monoclonal-antibody-s2h97
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD (without glycosylation) (1.9 ms)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-apo-sars-cov-2-spike-rbd-without-glycosylation
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: "SARS-CoV-2 spike RBD (with glycosylation) (1.8 ms)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-apo-sars-cov-2-spike-rbd-with-glycosylation
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
- Title: " SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2 (953.7 µs)"
URL: https://covid.molssi.org//simulations/#foldinghome-simulations-of-the-sars-cov-2-spike-rbd-with-n501y-mutation-bound-to-human-ace2
AuthorName: "The Chodera lab at the Memorial Sloan Kettering Cancer Center"
AuthorURL: https://choderalab.org
Tutorials:
- Title: "Folding@home COVID-19 efforts"
URL: https://github.com/FoldingAtHome/coronavirus/blob/master/README.md
AuthorName: "Folding@home Consortium"
Publications:
- Title: "SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome"
URL: https://doi.org/10.1101/2020.06.27.175430
AuthorName: "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"
- Title: "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity"
URL: https://doi.org/10.1016/j.cell.2021.01.037
AuthorName: "Emma C. Thomson, Laura E, Rosen, James G. Shepherd, et al."
- Title: "SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape"
URL: https://doi.org/10.1038/s41586-021-03807-6
AuthorName: "Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, et al."