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Lecturer(s)
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Berka Karel, doc. RNDr. Ph.D.
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Polishchuk Pavlo, M.Sc., Ph.D.
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Course content
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Drug design is a rather new approach towards rational search for new bioactive compounds. It is consisted from whole range of computational methods, which can be used to pre-select potential compounds for biological screening. Course will be delivered in a series of lectures and also hands-on tutorials to give students the possibility to try discussed methods on their own; 1. Introduction to rational drug design 2. Drug design discovery 3. Pharmacological and physical chemical properties 4. Tutorial: Software - calculation of properties, web applications and databases 5. Pharmaceutical target and structure of biomolecules 6. Tutorial: Visualisation of structure, PDB database, structure files, electron density 7. Docking, molecular mechanics and dynamics 8. Tutorial: Docking and molecular mechanics and dynamics 9. Methods for calculation of binding free energy, IC50, and inhibition constant 10. Tutorial: scoring functions 11. Tutorial: advanced methods for calculation of binding free energy 12. Future challenges in in silico drug design Lecture is follow-up to Radional Drug Design (KFC/DD)
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Training in job and motor Skils
- Preparation for the Exam
- 60 hours per semester
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Learning outcomes
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The students will deepen practical skills in in silico drug design.
To describe main methods used in drug design, to use methods on example.
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Prerequisites
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Student should be studying master degree or higher.
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Assessment methods and criteria
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Oral exam
Short drug design project on the student's suggestion, to show ability to discuss drug design methodology.
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Recommended literature
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Abraham, D.J., Rotella, P.R. (2010). Burger's Medicinal Chemistry, Drug Discovery and Development (7th edition). Wiley.
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Alvarez, J. & Shoichet B. (Eds.). (2005). Virtual Screening in Drug Discovery. Taylor&Francis.
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Krogsgaard-Larsen, P., Stromgaard, K., Madsen, U. (2010). Textbook of Drug Design and Discovery (4th Ed.). CRC Press.
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Leach AR. (2001). Molecular Modelling - Principles and Applications (2 edition). Pearson Education.
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Young, D.C. (2009). Computational Drug Design. Wiley.
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Young D.C. (2001). Computational Chemistry, a Practical Guide for Applying Techniques to Real World Problems. Wiley.
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