Admission requirements
Course course in MSc Chemistry for Health. Elective course in MSc Life Science and Technology, MSc Chemistry for Sustainability.
Description
This course provides an in-depth introduction to experimental and computational methods used to determine and analyze protein structures with a focus on their applications in drug discovery. Protein structures play a central role in understanding biological function at the molecular level and are pivotal for the rational design of therapeutics. With the advent of high-resolution structural techniques and advanced modeling tools, the ability to visualize proteins in atomic detail has never been more accessible - or more important.
Students will learn how to determine protein structures using cryo-electron microscopy (cryo-EM) and X-ray crystallography, as well as how to predict protein structures computationally using tools like AlphaFold. The course emphasizes practical aspects, such as data processing, model building, and structure interpretation. Through hands-on sessions and topical literature seminars, students will gain a robust toolkit for modeling and visualizing macromolecules, and will learn to critically evaluate structural data in the context of biomedical research and drug design.
Course Objectives
At the end of this course the student is able to:
Cryo-Electron Microscopy (Cryo-EM):
Describe the fundamental principles of cryo-EM and its application in structural biology.
Explain the steps of sample preparation, data acquisition, and image processing.
Evaluate cryo-EM data quality and evaluate 2D and 3D classification.
Apply integrative modeling techniques to build atomic models from cryo-EM maps.
Interpret cryo-EM structures in the context of drug discovery.
X-ray Crystallography:
Explain the process of protein crystallization and symmetry principles in crystals.
Process diffraction data using XDS and solve structures using molecular replacement.
Perform structure refinement using Phenix and assess model quality.
Conduct manual model building and interpretation of electron density maps using Coot.
Understand the application of crystallography in fragment-based drug discovery.
Structure Prediction:
Explain the principles of structure prediction by co-evolution and machine learning.
Evaluate the reliability of predicted protein structures using appropriate bioinformatics tools.
Use AlphaFold and related tools for structure-based hypothesis generation.
Modeling and Visualization of Macromolecules:
Create publication-quality molecular figures and animations using ChimeraX
Integrate experimental and predicted data for comprehensive structural interpretation.
Visualize protein-ligand interactions
Scientific Communication:
- Analyze and present primary literature in topical seminars
Timetable
Schedule information can be found on the website of the programmes.
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
Mode of Instruction
Lectures, seminars, practical exercises
Assessment method
Students will be evaluated based on a final exam (80%) and presentations (in groups) in student seminars, where they will discuss structural biology publications related to disease-relevant topics.
Reading list
- Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models (3rd edition)
- Single-particle Cryo-EM of Biological Macromolecules, Glaeser Nogales and Chiu (2021)
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Dr. S.R.J. Geibel, Dr. S. Brünle, Dr Z.W.B. Armstrong
Remarks
According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.