Molecular Modeling for Drug Design B – laboratory 1200-1CHMMOBL6
During the laboratory, students will be able to learn how to use the molecular modeling and visualization programs for chemical and biological molecules (e.g. Yasara, VMD, PyMol). Part of the programs will include the possibility of building and modifying chemical compounds and proteins. The exercises will also help to acquire the ability to use online databases of chemical compounds and their molecular targets (e.g. PubMed and PDB). Acquiring programming skills in Python will allow to perform, among others an exercise on the use of artificial intelligence methods (deep learning) for the classification of big data.
Students from group B will additionally (compared to group A) complete three exercises covering, among others, the use of Python scripts to create interactive graphs and the construction of protein and protein complex structures using artificial intelligence (AlphaFold3 server).
- Total student workload: 3*25 = 75 hours.
- Class participation: 45 hours
- Preparing for classes: 20 hours
- Consultations with instructors: 10 hours
Course coordinators
Type of course
Mode
Remote learning
Requirements
Prerequisites
Prerequisites (description)
Learning outcomes
KNOWLEDGE: Upon completing the course, the student knows and understands:
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To an advanced degree, the aspects of drug structure, mechanism of action, and synthesis, and understands the interdisciplinary nature of designing new drugs and drug delivery systems. The student also knows the fundamentals of molecular modeling.
SKILLS: Upon completing the course, the student is able to:
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Apply the conceptual framework and qualitative models of quantum chemistry to analyze and interpret the properties of atoms and molecules, as well as the course of simple chemical reactions; in particular:
apply the conceptual framework and qualitative models of chemistry to analyze and interpret the properties of molecules and their interactions with biomolecules;
search for necessary information in online databases of chemical compound and biomolecular structures, and use the Python programming language at a basic level.
Assessment criteria
Acceptable number of excused absences: it is required to pass all exercises, also on additional dates.
A grade is given for completing the exercise and reporting. Failure to pass the report will result in the exercise being repeated
The report is written and submitted during class.
Practical placement
N/A
Bibliography
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