Computer-aided drug design 1200-2CHMMO1W1
During the lecture, the assumptions of drug design methods and examples of their use will be discussed. To show a broader context of the application of these methods, a review of various molecular targets (proteins, DNA, RNA) with ligands/drugs will be made in order to compare their bioactive conformations, the role of individual interactions in the drug binding energy, the role of water molecules and the role of entropy in the drug binding process.
A typical vHTS (virtual high-throughput screening) experiment and its individual components will be presented, i.e. molecular docking with an overview of algorithms and software, the use of chemical databases, comparison and evaluation of ligand-receptor conformation using various evaluation methods, confusion matrix, ROC curves, AUC and the enrichment factor. In addition, the machine learning methods in drug design will be presented, as well as the FEP (free energy perturbation) method for the accurate determination of differences in drug binding strength.
Methods used in the absence of knowledge of the structure of molecular target, based on properties of ligands themselves (pharmacophore), design of peptide drugs and peptidomimetics, as well as the properties and design of antibodies will also be presented.
Main fields of studies for MISMaP
computer science
biology
physics
chemistry
mathematics
Type of course
Mode
Blended learning
Prerequisites
Prerequisites (description)
Course coordinators
Learning outcomes
Knowledge: the student knows and understands the major methods used in drug design. He knows the limitations of individual methods in terms of their accuracy and speed. He uses his knowledge to select the appropriate methods, or their combinations, for the selected molecular targets.
Skills: the student is able to formulate a research hypothesis, make a critical analysis of the results, and make conclusions based on them.
Social competences: the student understands and appreciates the importance of intellectual honesty in own and other people's activities; can think and act in an entrepreneurial manner; is able to use the acquired knowledge in other, related fields.
Assessment criteria
Requirements related to participation in class - none.
Permitted number of justified absences – 1 per 7 lectures.
Test exam with about 50% of closed questions and 50% of open questions -
the same for the correction test.
Required minimum 50% of correct answers to pass.
Practical placement
N/A
Bibliography
Recommended reading:
Graham L. Patrick, “An introduction to medicinal chemistry”, Oxford University Press, 2009; or newer.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: