Virtual Boot Camp: COVID ‐19 evolution and structural biology

Burley, Stephen K.; Bromberg, Yana; Craig, Paul; Duffy, Siobain; Dutta, Shuchismita; Hall, Bonnie L.; Hudson, Brian P.; Jiang, Jennifer; D Khare, Sagar; Koeppe, Julia R.; Lubin, Joseph H.; Mills, Stephen A.; Pikaart, Michael J.; Roberts, Rebecca; Sarma, Vidur; Singh, Jitendra; Tischfield, Jay A.; Xie, Lingjun; Zardecki, Christine

doi:10.1002/bmb.21428

Title: Virtual Boot Camp: COVID ‐19 evolution and structural biology

Abstract

COVID-19-related campus closures necessitated invention of an intensive online learning experience that introduced students to Structural Bioinformatics. The program engaged 33 students from 11 different institutions ranging from high school to graduate school. The objectives of the intensive, 1-week Boot Camp focused on helping students build a foundation for studying the SARS-CoV-2 Main Protease (Nsp5) to understand how the protein evolved during the first 6 months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools. Participants analyzed how the protein changed as the virus spread around the world, comparing Nsp5 from the original viral isolate to 161 unique sequence/structure variants.

Authors:

^[1]; Bromberg, Yana ^[2];

^[3]; Duffy, Siobain ^[4];

^[5];

^[6]; Hudson, Brian P. ^[5]; Jiang, Jennifer ^[7]; D Khare, Sagar ^[8]; Koeppe, Julia R. ^[9];

^[10]; Mills, Stephen A. ^[11];

^[12];

^[13]; Sarma, Vidur ^[7]; Singh, Jitendra ^[14]; Tischfield, Jay A. ^[15]; Xie, Lingjun ^[7];

^[5]

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey Piscataway New Jersey USA, Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center University of California, San Diego La Jolla California USA, Rutgers Cancer Institute of New Jersey, Rutgers The State University of New Jersey New Brunswick New Jersey USA
Department of Biochemistry and Microbiology Rutgers University New Brunswick New Jersey USA
School of Chemistry &, Materials Science Rochester Institute of Technology Rochester New York USA
Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey New Brunswick New Jersey USA
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey Piscataway New Jersey USA
Department of Chemistry Grand View University Des Moines Iowa USA
Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey Piscataway New Jersey USA
Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey Piscataway New Jersey USA, Department of Chemistry &, Chemical Biology Rutgers University Piscataway New Jersey USA
Chemistry State University of New York at Oswego Oswego New York USA
Department of Chemistry &, Chemical Biology Rutgers University Piscataway New Jersey USA
Chemistry Department Xavier University Cincinnati Ohio USA
Department of Chemistry and Biochemistry Hope College Holland Michigan USA
Biology Department Ursinus College Collegeville Pennsylvania USA
CUNY New York City College of Technology New York New York USA
Department of Genetics Rutgers University Piscataway New Jersey USA, Human Genetics Institute of New Jersey Piscataway New Jersey USA

Publication Date:: Fri Aug 14 00:00:00 EDT 2020

Research Org.:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Org.:: USDOE Office of Science (SC); National Science Foundation (NSF); National Cancer Institute (NCI); National Institute of Allergy and Infectious Diseases (NIAID); National Institute of General Medical Sciences (NIGMS)

OSTI Identifier:: 1669726

Alternate Identifier(s):: OSTI ID: 1669727; OSTI ID: 1803878

Grant/Contract Number:: DE‐SC0019749; SC0019749; DBI-1832184; R01GM133198; IUSE 1709170; 1709355; 1709805; 1709278; NIH T32 GM008339

Resource Type:: Published Article

Journal Name:: Biochemistry and Molecular Biology

Additional Journal Information:: Journal Name: Biochemistry and Molecular Biology Journal Volume: 48 Journal Issue: 5; Journal ID: ISSN 1470-8175

Publisher:: Wiley Blackwell (John Wiley & Sons)

Country of Publication:: Netherlands

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; biochemistry & molecular biology; education & educational research

Citation Formats


                    Burley, Stephen K., Bromberg, Yana, Craig, Paul, Duffy, Siobain, Dutta, Shuchismita, Hall, Bonnie L., Hudson, Brian P., Jiang, Jennifer, D Khare, Sagar, Koeppe, Julia R., Lubin, Joseph H., Mills, Stephen A., Pikaart, Michael J., Roberts, Rebecca, Sarma, Vidur, Singh, Jitendra, Tischfield, Jay A., Xie, Lingjun, and Zardecki, Christine. Virtual Boot Camp: COVID ‐19 evolution and structural biology.  Netherlands: N. p., 2020. 
Web.  doi:10.1002/bmb.21428.

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                    Burley, Stephen K., Bromberg, Yana, Craig, Paul, Duffy, Siobain, Dutta, Shuchismita, Hall, Bonnie L., Hudson, Brian P., Jiang, Jennifer, D Khare, Sagar, Koeppe, Julia R., Lubin, Joseph H., Mills, Stephen A., Pikaart, Michael J., Roberts, Rebecca, Sarma, Vidur, Singh, Jitendra, Tischfield, Jay A., Xie, Lingjun, & Zardecki, Christine. Virtual Boot Camp: COVID ‐19 evolution and structural biology.  Netherlands.  https://doi.org/10.1002/bmb.21428

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                    Burley, Stephen K., Bromberg, Yana, Craig, Paul, Duffy, Siobain, Dutta, Shuchismita, Hall, Bonnie L., Hudson, Brian P., Jiang, Jennifer, D Khare, Sagar, Koeppe, Julia R., Lubin, Joseph H., Mills, Stephen A., Pikaart, Michael J., Roberts, Rebecca, Sarma, Vidur, Singh, Jitendra, Tischfield, Jay A., Xie, Lingjun, and Zardecki, Christine. Fri .  
"Virtual Boot Camp: COVID ‐19 evolution and structural biology".  Netherlands.  https://doi.org/10.1002/bmb.21428.

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@article{osti_1669726,

  title        = {Virtual Boot Camp: COVID ‐19 evolution and structural biology},

  author       = {Burley, Stephen K. and Bromberg, Yana and Craig, Paul and Duffy, Siobain and Dutta, Shuchismita and Hall, Bonnie L. and Hudson, Brian P. and Jiang, Jennifer and D Khare, Sagar and Koeppe, Julia R. and Lubin, Joseph H. and Mills, Stephen A. and Pikaart, Michael J. and Roberts, Rebecca and Sarma, Vidur and Singh, Jitendra and Tischfield, Jay A. and Xie, Lingjun and Zardecki, Christine},

  abstractNote = {COVID-19-related campus closures necessitated invention of an intensive online learning experience that introduced students to Structural Bioinformatics. The program engaged 33 students from 11 different institutions ranging from high school to graduate school. The objectives of the intensive, 1-week Boot Camp focused on helping students build a foundation for studying the SARS-CoV-2 Main Protease (Nsp5) to understand how the protein evolved during the first 6 months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools. Participants analyzed how the protein changed as the virus spread around the world, comparing Nsp5 from the original viral isolate to 161 unique sequence/structure variants.},

  doi          = {10.1002/bmb.21428},

  journal      = {Biochemistry and Molecular Biology},

  number       = 5,

  volume       = 48,

  place        = {Netherlands},

  year         = {Fri Aug 14 00:00:00 EDT 2020},

  month        = {Fri Aug 14 00:00:00 EDT 2020}

}

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Works referenced in this record:

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018

Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
Nucleic Acids Research, Vol. 47, Issue D1
DOI: 10.1093/nar/gky1004

Flexible Implementation of the BASIL CURE
journal, June 2019

Roberts, Rebecca; Hall, Bonnie; Daubner, Colette
Biochemistry and Molecular Biology Education, Vol. 47, Issue 5
DOI: 10.1002/bmb.21287

The EMBL-EBI search and sequence analysis tools APIs in 2019
journal, April 2019

Madeira, Fábio; Park, Young mi; Lee, Joon
Nucleic Acids Research, Vol. 47, Issue W1
DOI: 10.1093/nar/gkz268

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
journal, May 2017

Kleffner, Robert; Flatten, Jeff; Leaver-Fay, Andrew
Bioinformatics, Vol. 33, Issue 17
DOI: 10.1093/bioinformatics/btx283

The Protein Data Bank
journal, January 2000

Berman, H. M.
Nucleic Acids Research, Vol. 28, Issue 1
DOI: 10.1093/nar/28.1.235

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Title: Virtual Boot Camp: COVID ‐19 evolution and structural biology

Abstract

Citation Formats

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy journal, October 2018

Flexible Implementation of the BASIL CURE journal, June 2019

The EMBL-EBI search and sequence analysis tools APIs in 2019 journal, April 2019

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta journal, May 2017

The Protein Data Bank journal, January 2000

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018

Flexible Implementation of the BASIL CURE
journal, June 2019

The EMBL-EBI search and sequence analysis tools APIs in 2019
journal, April 2019

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
journal, May 2017

The Protein Data Bank
journal, January 2000