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Bhagesh Hunakunti
In this 1-hour long project-based course, you will construct a 3D structure of a SARS-CoV-2 protein sequence using homology modeling and perform molecular docking of drugs against this protein molecule and infer protein-drug interaction. We will accomplish it in by completing each task in the project which includes
- Model protein structures from sequence data
- Process proteins and ligands for docking procedure
- Molecular docking of drugs against protein molecules
Read more
In this 1-hour long project-based course, you will construct a 3D structure of a SARS-CoV-2 protein sequence using homology modeling and perform molecular docking of drugs against this protein molecule and infer protein-drug interaction. We will accomplish it in by completing each task in the project which includes
- Model protein structures from sequence data
- Process proteins and ligands for docking procedure
- Molecular docking of drugs against protein molecules
Read more
In this 1-hour long project-based course, you will construct a 3D structure of a SARS-CoV-2 protein sequence using homology modeling and perform molecular docking of drugs against this protein molecule and infer protein-drug interaction. We will accomplish it in by completing each task in the project which includes
- Model protein structures from sequence data
- Process proteins and ligands for docking procedure
- Molecular docking of drugs against protein molecules
Note: This course works best for learners who are based in the North America region. We’re currently working on providing the same experience in other regions.
Register for this course and see more details by visiting:
OpenCourser.com/course/n09is4/sars
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What's inside
Syllabus
Traffic lights
Traffic lights
Read about what's good
what should give you pause and
possible dealbreakers
Appropriate for students interested in learning how to infer protein-drug interactions in drug screening and discovery
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Reviews summary
Hands-on sars-cov-2 protein modeling
According to students, this project-based course offers a highly practical introduction to SARS-CoV-2 protein modeling and drug docking. Learners frequently commend the clear, step-by-step guidance and the opportunity for hands-on application of techniques like homology modeling and molecular docking. While generally well-received, some learners note the fast pace and that prior knowledge in molecular biology or computational methods is beneficial. A specific concern highlighted by some is the regional restriction for North America, which can affect the smooth execution for learners outside this area. Overall, it's considered an excellent, concise resource for specific skill development in computational drug discovery.
A short course, provides a foundational overview.
"It's an excellent project to learn the basics of protein modeling within a very short timeframe."
"For just one hour, it covers a surprising amount of practical material that is directly applicable."
"I found it a great introduction, but it doesn't delve into advanced topics like computational chemistry in depth."
Instructions are easy to follow for complex tasks.
"The instructor's explanations made complex topics accessible and easy to follow, even for a beginner."
"Every step was clearly demonstrated, which was crucial for setting up the simulations correctly."
"I appreciated the methodical approach to setting up and running the docking simulations from start to finish."
Offers direct experience with modeling and docking.
"This course provided me with a solid foundation in computational drug design through practical exercises."
"The hands-on activities were incredibly helpful for understanding molecular docking processes."
"I found the project-based approach very effective for applying homology modeling to real-world scenarios."
Some technical issues reported outside North America.
"As someone outside North America, I encountered issues with software access or platform compatibility that hindered my progress."
"The regional restriction made it challenging to complete the project smoothly from my location, which was frustrating."
"I wish the course had broader support for learners globally, not just North America, to ensure wider accessibility."
Assumes foundational understanding; moves at a fast pace.
"I recommend having some basic molecular biology or computational chemistry background before starting this project."
"The pace is quite fast for a beginner; it would be good to have prior experience with bioinformatics tools."
"Though short, the course assumes familiarity with concepts like protein structure and ligand preparation, which is fair for a project."
Activities
Be better prepared
before
your course. Deepen your understanding
during
and
after
it. Supplement your coursework and achieve mastery of the topics covered
in SARS-CoV-2 Protein Modeling and Drug Docking with these
activities:
Gather online notes and resources for subsequent review.
Show steps
The course has a lot of online materials. This activity encourages learners to be proactive about gathering the materials they will need to study.
Browse courses on
Review
Show steps
-
Locate and save lecture notes from the online course materials.
-
Gather the handouts and supplementary materials.
-
Organize the materials in a way that makes sense to you.
Watch a tutorial on homology modeling.
Show steps
Homology modeling pipelines are part of the course. This activity will help set students up for success by learning how to use them.
Show steps
-
Find a tutorial on homology modeling.
-
Watch the tutorial.
-
Follow the steps in the tutorial to build a homology model.
Watch a tutorial on molecular docking.
Show steps
Molecular Docking Software is covered in the course. This activity provides another perspective on how these tools are used.
Browse courses on
Molecular Docking
Show steps
-
Watch the tutorial.
-
Find a tutorial on molecular docking.
-
Follow the steps in the tutorial to dock a ligand to a protein.
Eight other activities
Expand to see all activities and additional details
Show all 11 activities
Practice Questions: Protein Structure and Function
Show steps
Solving practice questions will help you reinforce your understanding of protein structure and function, which are key concepts in this course.
Browse courses on
Protein Structure
Show steps
-
Answer the questions
-
Check your answers
-
Review the explanations
Study Group: Protein Modeling and Molecular Docking
Show steps
Participating in a study group will allow you to discuss the course material with your peers, ask questions, and share your knowledge.
Show steps
-
Find a study group or start your own
-
Meet regularly to discuss the course material
-
Work together on projects and assignments
Tutorial: Molecular Docking with AutoDock Vina
Show steps
This tutorial will provide you with a step-by-step guide to molecular docking using AutoDock Vina, which is a widely used software for this purpose.
Browse courses on
Molecular Docking
Show steps
-
Install AutoDock Vina
-
Prepare the protein and ligand files
-
Run the docking
-
Analyze the results
Design a Protein Model
Show steps
This project will provide you with hands-on experience in protein modeling and molecular docking, which are essential techniques in drug discovery.
Show steps
-
Prepare the protein sequence and template structure
-
Build the homology model
-
Validate the model
-
Dock the drugs to the protein
-
Analyze the docking results
Build 5-10 small protein structure models using homology modeling.
Show steps
The course will cover topics in homology modeling and molecular docking. Gaining proficiency through practice will help solidify this knowledge.
Show steps
-
Gather protein data.
-
Sequence alignment and template selection
-
Build homology model
-
Model evaluation
Dock 5-10 small molecules to the protein.
Show steps
The course covers how to perform molecular docking. Completing this activity will reinforce these techniques.
Browse courses on
Molecular Docking
Show steps
-
Prepare protein and ligand for docking.
-
Perform docking.
-
Analyze docking results.
Find a mentor who can provide guidance on homology modeling and molecular docking.
Show steps
These modeling and docking techniques are complex. Working with a mentor who has expertise can greatly improve understanding and retention.
Show steps
-
Identify potential mentors.
-
Contact potential mentors and introduce yourself.
-
Set up regular meetings with your mentor.
-
Discuss your progress in the course with your mentor.
-
Seek feedback from your mentor on your work.
Analyze the results of molecular docking experiments.
Show steps
Students will perform several molecular docking experiments in the course. This activity gives them an opportunity to reflect on these experiments and gain deeper insights.
Browse courses on
Molecular Docking
Show steps
-
Examine the binding modes of the docked molecules.
-
Identify the key interactions between the protein and the ligand.
-
Predict the biological activity of the docked molecules.
Gather online notes and resources for subsequent review.
Show steps
The course has a lot of online materials. This activity encourages learners to be proactive about gathering the materials they will need to study.
Browse courses on
Review
Show steps
Show steps
Show steps
- Locate and save lecture notes from the online course materials.
- Gather the handouts and supplementary materials.
- Organize the materials in a way that makes sense to you.
Watch a tutorial on homology modeling.
Show steps
Homology modeling pipelines are part of the course. This activity will help set students up for success by learning how to use them.
Show steps
Show steps
Show steps
- Find a tutorial on homology modeling.
- Watch the tutorial.
- Follow the steps in the tutorial to build a homology model.
Watch a tutorial on molecular docking.
Show steps
Molecular Docking Software is covered in the course. This activity provides another perspective on how these tools are used.
Browse courses on
Molecular Docking
Show steps
Show steps
Show steps
- Watch the tutorial.
- Find a tutorial on molecular docking.
- Follow the steps in the tutorial to dock a ligand to a protein.
Eight other activities
Expand to see all activities and additional details
Show all 11 activities
Practice Questions: Protein Structure and Function
Show steps
Solving practice questions will help you reinforce your understanding of protein structure and function, which are key concepts in this course.
Browse courses on
Protein Structure
Show steps
Show steps
Show steps
- Answer the questions
- Check your answers
- Review the explanations
Study Group: Protein Modeling and Molecular Docking
Show steps
Participating in a study group will allow you to discuss the course material with your peers, ask questions, and share your knowledge.
Show steps
Show steps
Show steps
- Find a study group or start your own
- Meet regularly to discuss the course material
- Work together on projects and assignments
Tutorial: Molecular Docking with AutoDock Vina
Show steps
This tutorial will provide you with a step-by-step guide to molecular docking using AutoDock Vina, which is a widely used software for this purpose.
Browse courses on
Molecular Docking
Show steps
Show steps
Show steps
- Install AutoDock Vina
- Prepare the protein and ligand files
- Run the docking
- Analyze the results
Design a Protein Model
Show steps
This project will provide you with hands-on experience in protein modeling and molecular docking, which are essential techniques in drug discovery.
Show steps
Show steps
Show steps
- Prepare the protein sequence and template structure
- Build the homology model
- Validate the model
- Dock the drugs to the protein
- Analyze the docking results
Build 5-10 small protein structure models using homology modeling.
Show steps
The course will cover topics in homology modeling and molecular docking. Gaining proficiency through practice will help solidify this knowledge.
Show steps
Show steps
Show steps
- Gather protein data.
- Sequence alignment and template selection
- Build homology model
- Model evaluation
Dock 5-10 small molecules to the protein.
Show steps
The course covers how to perform molecular docking. Completing this activity will reinforce these techniques.
Browse courses on
Molecular Docking
Show steps
Show steps
Show steps
- Prepare protein and ligand for docking.
- Perform docking.
- Analyze docking results.
Find a mentor who can provide guidance on homology modeling and molecular docking.
Show steps
These modeling and docking techniques are complex. Working with a mentor who has expertise can greatly improve understanding and retention.
Show steps
Show steps
Show steps
- Identify potential mentors.
- Contact potential mentors and introduce yourself.
- Set up regular meetings with your mentor.
- Discuss your progress in the course with your mentor.
- Seek feedback from your mentor on your work.
Analyze the results of molecular docking experiments.
Show steps
Students will perform several molecular docking experiments in the course. This activity gives them an opportunity to reflect on these experiments and gain deeper insights.
Browse courses on
Molecular Docking
Show steps
Show steps
Show steps
- Examine the binding modes of the docked molecules.
- Identify the key interactions between the protein and the ligand.
- Predict the biological activity of the docked molecules.
Career center
Learners who complete SARS-CoV-2 Protein Modeling and Drug Docking will develop knowledge and skills
that may be useful to these careers:
Biochemist
Biochemist
Biochemists study the chemical processes that occur in living organisms. This course delves into protein modeling and docking, techniques that are commonly employed by Biochemists to investigate the structure and function of proteins at the molecular level.
Pharmacologist
Pharmacologist
Pharmacologists study the effects of drugs on living organisms. This course offers practical experience in molecular docking, a technique used to predict drug-target interactions. Understanding molecular docking is essential for Pharmacologists involved in drug discovery and development.
Molecular Biologist
Molecular Biologist
Molecular Biologists study the structure and function of biological molecules, including proteins. This course provides hands-on experience in protein modeling and docking, techniques that are frequently utilized by Molecular Biologists to investigate protein structure and interactions at the molecular level.
Virologist
Virologist
Virologists study viruses and their interactions with living organisms. This course provides a foundation in protein modeling and docking, techniques that are commonly employed by Virologists to investigate the structure and function of viral proteins and their interactions with host factors.
Computational Biologist
Computational Biologist
Computational Biologists apply computational and analytical approaches to address biological questions and advance our understanding of living systems. This course can help enhance foundational knowledge in protein modeling and docking techniques commonly employed by Computational Biologists in their research.
Biophysicist
Biophysicist
Biophysicists use physical principles and techniques to study biological systems at the molecular and cellular levels. This course covers protein modeling and docking, which are commonly employed by Biophysicists to investigate the structure and dynamics of biological molecules.
Bioinformatics Scientist
Bioinformatics Scientist
A Bioinformatics Scientist develops and utilizes computational and statistical techniques to analyze biological data and solve biological problems. Completing this course will help build a foundation for homology modeling and molecular docking, essential skills that are commonly employed by Bioinformatics Scientists to study protein structures and interactions.
Chemist
Chemist
Chemists study the composition, structure, properties, and reactions of matter. This course delves into molecular docking, a technique used to predict the binding interactions between molecules. Understanding molecular docking can be beneficial for Chemists, particularly those working in drug discovery and development.
Microbiologist
Microbiologist
Microbiologists study microorganisms and their interactions with living organisms. This course offers insights into protein modeling and docking, techniques that can be applied in microbiology research, particularly in areas such as understanding the molecular mechanisms of infectious diseases.
Biomedical Engineer
Biomedical Engineer
Biomedical Engineers apply engineering principles and techniques to solve problems in biology and medicine. This course provides insights into protein modeling and drug docking, which can be relevant to the development of biomedical devices, diagnostics, and therapies.
Toxicologist
Toxicologist
Toxicologists assess the effects of chemical substances on living organisms and the environment. This course provides foundational knowledge in protein modeling and docking, techniques that can aid Toxicologists in understanding the interactions between toxicants and biological systems.
Computer Scientist
Computer Scientist
Computer Scientists design and develop software and systems to solve computational problems. This course introduces techniques in homology modeling and molecular docking, which are relevant to the field of bioinformatics and computational biology, areas where Computer Scientists often contribute.
Data Scientist
Data Scientist
Data Scientists use data analysis techniques to extract insights from data. This course provides hands-on experience in protein modeling and docking, data-intensive techniques that can be incorporated into the toolkit of Data Scientists working in the fields of bioinformatics and computational biology.
Epidemiologist
Epidemiologist
Epidemiologists study the distribution and patterns of health-related states and events in populations. While not directly related to epidemiology, this course may provide foundational knowledge in protein modeling and docking techniques that could be applied in research areas such as infectious disease modeling.
Physician
Physician
Physicians diagnose and treat diseases and injuries. While not directly related to clinical practice, this course may be of interest to Physicians who are involved in research, particularly in areas such as drug discovery and development, where knowledge of protein modeling and docking can be beneficial.
For more career information including salaries, visit:
OpenCourser.com/course/n09is4/sars
Reading list
We've selected six books
that we think will supplement your
learning. Use these to
develop background knowledge, enrich your coursework, and gain a
deeper understanding of the topics covered in
SARS-CoV-2 Protein Modeling and Drug Docking.
Save
This classic biochemistry textbook provides a comprehensive overview of the field, including chapters on protein structure and function, enzyme kinetics, and drug discovery. It valuable reference for anyone working in the field of drug development.
Provides a comprehensive overview of the drug discovery and development process, including sections on target identification, lead optimization, and clinical trials. It valuable resource for anyone interested in learning more about the process of bringing new drugs to market.
Provides a comprehensive overview of the field of medicinal chemistry, including chapters on drug design, synthesis, and evaluation. It valuable resource for anyone interested in learning more about the development of new drugs.
Save
Provides a comprehensive overview of the field of cancer biology, including chapters on cancer cell growth and proliferation, cancer metastasis, and cancer therapy. It valuable resource for anyone interested in learning more about the molecular basis of cancer.
Provides a comprehensive overview of the field of pathophysiology, including chapters on the cardiovascular system, the respiratory system, and the immune system. It valuable resource for anyone interested in learning more about the molecular basis of disease.
Provides a solid foundation in protein structure and function, which is essential for understanding the molecular basis of drug interactions. It covers topics such as protein folding, protein-protein interactions, and enzyme catalysis.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/n09is4/sars
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