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Tags: PDB

All Categories (1-18 of 18)

  1. Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2

    18 Jul 2020 | Teaching Materials | Contributor(s):

    By Maria Shumskaya1, Nicholas Lorusso2

    1. Kean University 2. Kean Univeristy

    Introduction into computational approaches in phylogeny and protein modeling based on coronavirus SARS-CoV-2 (caused COVID-19 pandemic). Two self-guided tutorials for standard lab classes of 2.5...

    https://qubeshub.org/publications/1796/?v=2

  2. CRISPR Gene Editing: Designing the gRNA and Donor Template

    15 Jul 2020 | Teaching Materials | Contributor(s):

    By Laurel Lorenz

    Princeton

    In this adaptation, students learn how CRISPR/Cas9 is used in bacterial immunity and gene editing. Students create both a gRNA target and a donor template to edit a gene. Mutations can be from the...

    https://qubeshub.org/publications/1962/?v=1

  3. Understanding COVID-19 Biology to Design a Vaccine - Ethics supplement

    08 Jul 2020 | Teaching Materials | Contributor(s):

    By Keith A. Johnson

    Bradley University College of Liberal Arts and Sciences

    The adaptation to Understanding COVID-19 Biology to Design a Vaccine entails two ethics supplements. The first supplement addresses the use of off-label drugs in the pandemic (or other situation)....

    https://qubeshub.org/publications/1955/?v=1

  4. COVID-19: Molecular Basis of Infection-ADAPTATION

    17 Jun 2020 | Teaching Materials | Contributor(s):

    By Didem Vardar-Ulu

    Boston University, Chemistry Department

    This case was written in Spring 2020 during the COVID-19 pandemic. It focuses on understanding the structure and interaction of the SARS-Cov-2 viral spike protein that facilitates infection in...

    https://qubeshub.org/publications/1936/?v=1

  5. Drugging SARS-CoV-2

    15 Jun 2020 | Teaching Materials | Contributor(s):

    By Mallory Bliss1, Alexzandria Khan1, Nandni Verma1, Kasandra Jean-Louise Riley1

    Rollins College

    This case study leads students through the process of proposing a drug for a novel protein. The Mpro protease of SARS-CoV-2 is explored in detail within the PDB. Aligns with first semester...

    https://qubeshub.org/publications/1928/?v=1

  6. Molecular Basis of Sickle Cell Disease

    15 Jun 2020 | Teaching Materials | Contributor(s):

    By Didem Vardar-Ulu

    Boston University, Chemistry Department

    This multi part case on hemoglobin structure as it relates to oxygen binding and sickle cell disease focuses on utilizing bioinformatics and molecular visualization tools to learn about the sickle...

    https://qubeshub.org/publications/1925/?v=1

  7. The Happy Blue Baby Hemoglobin

    14 Jun 2020 | Teaching Materials | Contributor(s):

    By Kasandra Jean-Louise Riley1, Shuchismita Dutta2

    1. Rollins College 2. RCSB Protein Data Bank, Rutgers University

    This case, about a specific mutant of hemoglobin, focuses on visualizing and understanding the molecular basis of why an infant turned blue soon after birth and how the cyanosis resolved.

    https://qubeshub.org/publications/1924/?v=1

  8. Nicholas' Story

    13 Jun 2020 | Teaching Materials | Contributor(s):

    By Nik Tsotakos

    Penn State Harrisburg

    This 3 part case on sickle cell disease focuses on visualizing and understanding the molecular basis of its cause, symptoms, complications, management, treatment, and possible cures.

    https://qubeshub.org/publications/1919/?v=1

  9. COVID-19: On the way to a vaccine

    13 Jun 2020 | Teaching Materials | Contributor(s):

    By Nik Tsotakos

    Penn State Harrisburg

    This multi-part case study introduces the reader to the SARS-CoV-2 virus origins, the molecular basis of the infection, the development and severity of symptoms, and treatment.

    https://qubeshub.org/publications/1918/?v=1

  10. Understanding COVID-19 Biology to Design a Vaccine

    12 Jun 2020 | Teaching Materials | Contributor(s):

    By Keith Johnson1, Didem Vardar-Ulu2, Shuchismita Dutta3

    1. Bradley University College of Liberal Arts and Sciences 2. Boston University 3. RCSB Protein Data Bank, Rutgers University

    This multi-part case study introduces the reader to the SARS-CoV-2 virus, replication, and treatment. Additional worksheets introduce students to bioinformatics tools of 3-D protein visualization...

    https://qubeshub.org/publications/1904/?v=1

  11. COVID-19: Molecular Basis of Infection

    12 Jun 2020 | Teaching Materials | Contributor(s):

    By Didem Vardar-Ulu1, Shuchismita Dutta2

    1. Boston University 2. RCSB Protein Data Bank, Rutgers University

    This case was written in Spring 2020 during the COVID-19 pandemic. It focuses on understanding the structure and interaction of the SARS-Cov-2 viral spike protein that facilitates infection in...

    https://qubeshub.org/publications/1912/?v=1

  12. A Case of Severe Insulin Resistance

    12 Jun 2020 | Teaching Materials | Contributor(s):

    By Melanie Lenahan1, Shuchismita Dutta2

    1. Raritan Valley Community College 2. RCSB Protein Data Bank, Rutgers University

    This case focuses on understanding how a mutation in a cell signalling protein (a kinase) can prevent insulin function and lead to diabetes.

    https://qubeshub.org/publications/1911/?v=1

  13. Evolution of Caffeine Biosynthesis Enzymes

    12 Jun 2020 | Teaching Materials | Contributor(s):

    By Brian Sullivan1, Shuchismita Dutta2

    1. University of North Carolina 2. RCSB Protein Data Bank, Rutgers University

    This case focuses on exploring why plants make secondary metabolites like caffeine and how the enzymes required for making caffeine evolved.

    https://qubeshub.org/publications/1909/?v=1

  14. Piwi Matters

    12 Jun 2020 | Teaching Materials | Contributor(s):

    By Laurel Lorenz1, Shuchismita Dutta2

    1. Princeton University 2. RCSB Protein Data Bank, Rutgers University

    This case focuses on understanding structure and function relationships in Piwi, a protein that is critical for germline stem cell function and development of eggs in the fruit fly ovary.

    https://qubeshub.org/publications/1910/?v=1

  15. Waking up Anna

    11 Jun 2020 | Teaching Materials | Contributor(s):

    By Kate K. O'Toole1, Shuchismita Dutta2

    1. Emory University 2. RCSB Protein Data Bank, Rutgers University

    This case focuses on understanding the molecular basis of Anna's sleeping disorder and its treatment.

    https://qubeshub.org/publications/1908/?v=1

  16. Happy Blue Baby

    11 Jun 2020 | Teaching Materials | Contributor(s):

    By Shuchismita Dutta

    RCSB Protein Data Bank, Rutgers University

    This case, about a specific mutant of hemoglobin, focuses on visualizing and understanding the molecular basis of why an infant turned blue soon after birth and how the cyanosis resolved on its own...

    https://qubeshub.org/publications/1902/?v=1

  17. Nicholas' Story

    11 Jun 2020 | Teaching Materials | Contributor(s):

    By Shuchismita Dutta1, Kimberly Linenberger Cortes2, Henry Vincent Jakubowski3, Melanie Lenahan4, David Marcey5, Pat Marsteller6, Cassidy Terrell7

    1. RCSB Protein Data Bank, Rutgers University 2. Kennesaw State University 3. College of Saint Benedict/Saint John's University 4. Raritan Valley Community College 5. California Lutherian University 6. Emory University 7. University of Minnesota, Rocester

    This 3 part case on sickle cell disease focuses on visualizing and understanding the molecular basis of its cause, symptoms, complications, management, treatment, and possible cures.

    https://qubeshub.org/publications/1907/?v=1

  18. Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2

    03 Apr 2020 | Teaching Materials | Contributor(s):

    By Maria Shumskaya1, Nicholas Lorusso2

    1. Kean University 2. Kean Univeristy

    Introduction into computational approaches in phylogeny and protein modeling based on coronavirus SARS-CoV-2 (caused COVID-19 pandemic). Two self-guided tutorials for standard lab classes of 2.5...

    https://qubeshub.org/publications/1796/?v=1