Teaching Materials (1-20 of 25)

1. A "Box of Lessons" for Exploring Biomolecular Structure and Function

   20 Jul 2022 | Teaching Materials | Contributor(s):

   By Keith A. Johnson¹, Alexandra Pettit², Sheela Vemu³, Shuchismita Dutta⁴

   1. Bradley University College of Liberal Arts and Sciences 2. Carleton University 3. Waubonsee Community College - 4. RCSB Protein Data Bank, Rutgers University

   Biomolecular structure and function is emphasized as a core concept in a variety of community determined educational standards for biology and chemistry. Most curricula introduce students to the...

   https://qubeshub.org/publications/3448/?v=1

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

   03 Feb 2022 | Teaching Materials | Contributor(s):

   By Maria Shumskaya¹, Christopher Zambell¹, Nicholas Lorusso²

   1. Kean University 2. University of North Texas at Dallas

   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=3

3. Mol* Adaptation: Case of Severe Insulin Resistance

   23 Jul 2021 | Teaching Materials | Contributor(s):

   By Keith A. Johnson

   Bradley University College of Liberal Arts and Sciences

   This is an adaptation using Mol* on the original case written. This case focuses on understanding how a mutation in a cell signalling protein (a kinase) can prevent insulin function and lead to...

   https://qubeshub.org/publications/2483/?v=1

4. Happy Blue Baby

   09 Jun 2021 | Teaching Materials | Contributor(s):

   By Didem Vardar-Ulu

   Boston University, Chemistry Department

   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/2419/?v=1

5. COVID-19: Molecular Basis Infection Revisited One Year into the Pandemic

   09 Jun 2021 | Teaching Materials | Contributor(s):

   By Didem Vardar-Ulu

   Boston University, Chemistry Department

   This adaptation was written in Spring 2021 exactly one year after the original case and includes explorations of the emerging mutations within the spike protein

   https://qubeshub.org/publications/2424/?v=1

6. Waking up Anna - Adaptations and Conversion to Mol*

   08 Jun 2021 | Teaching Materials | Contributor(s):

   By Keith A. Johnson

   Bradley University College of Liberal Arts and Sciences

   This case focuses on understanding the molecular basis of Anna's sleeping disorder and its treatment.The adaptations addressed question clarity and reformatting to use Mol*.

   https://qubeshub.org/publications/2420/?v=1

7. Happy Blue Baby: MCQs for large classes

   18 May 2021 | Teaching Materials | Contributor(s):

   By "KP" Kristen Procko

   The University of Texas at Austin

   Multiple choice questions for the Happy Blue Baby case study pre-work

   https://qubeshub.org/publications/2381/?v=1

8. 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. University of North Texas at Dallas

   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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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