Molecular Modeling for Drug Design 1200-1CHMMOW6
Molecular modeling and visualization methods are currently one of the basic parts of drug design methodology. This is true both for drug design based on the structure of molecular target (structure-based drug design) and without this structure based only on active and inactive chemical compounds (ligand-based drug design). The lecture will discuss the basics of molecular modeling (CPK model), definition of the force field and its application in molecular mechanics and dynamics.
Programs for the visualization of chemical and biological molecules, building and modification of chemical compounds and proteins, as well as elements of programming will also be presented. An important part of drug design is also the ability to use online databases of chemical compounds and molecular targets (proteins, DNA, RNA) – it will be discussed which types of information are available there and how to use them.
- Total student workload: 1.5 * 30 = 45 hours.
- Class participation: 15 hours
- Preparing for classes and exam: 20 hours
- Consultations with lecturer: 10 hours
Type of course
Mode
Remote learning
Prerequisites
Prerequisites (description)
Course coordinators
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
Maximum number of absences to achieve learning outcomes - 1.
Course completion: a written exam with approximately 50% closed-ended questions and 50% open-ended questions. The same applies to the retake exam.
Required minimum 50% of correct answers to pass.
Practical placement
N/A
Bibliography
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Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: