FAMM1_12 Principles of Computational Chemistry and Molecular Modelling

Faculty of Pharmacy
Spring 2020
Extent and Intensity
1/1/0. 3 credit(s). Type of Completion: zk (examination).
Teacher(s)
Mgr. Ing. Jiří Václavík, Ph.D. (lecturer)
Mgr. Ing. Jiří Václavík, Ph.D. (seminar tutor)
Guaranteed by
Mgr. Ing. Jiří Václavík, Ph.D.
Department of Natural Drugs – Departments – Faculty of Pharmacy
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The subject is oriented to offer students essential overview about the modern approaches in R&D of new potential drugs using the computational chemistry and molecular modeling.
During the practical lessons students will learn how to use the basic and advanced techniques of computational chemistry, molecular graphics, and molecular modeling/design.
Syllabus
  • 1. The historical development of empirical and rational research and drug design. The history of molecular modeling and computational chemistry.
    Practical part: Work with primary and secondary sources of information focusing on the issues of molecular modeling (Bioinformatics), modeling, visualization of molecules and molecular graphics.
    2. Structure as a carrier of biological activity. The structure of biomacromolecules and structural methods.
    Practical part: Visualization of primary, secondary and tertiary structures of macromolecules. The molecular surfaces, the active sites of enzymes.
    3. Energy of the molecule. Theory and methods in molecular modeling calculations. Methods of molecular mechanics.
    Practical part: Working with the basic software for computational chemistry, e.g. ChemOffice, HyperChem, Gaussian, GAMESS. Calculations using the molecular mechanics methods.
    4. Semiempirical methods, ab initio methods, DFT and their use in computational chemistry.
    Practical part: Model calculations using semiempirical methods, ab initio and DFT methods using the ChemOffice Package, HyperChem, Gaussian and GAMESS. The allocation of tasks for individual dissertation.
    5. Methods of studying the interaction at the molecular level, homology modeling, the Brookhaven Protein Data Bank, The Cambridge Structural Database. Docking of ligands into active sites - critical factors pharmacophore.
    Practical part: Using protein databases, the database of sequences. Visualization of biomacromolecules using database interface. Fitting a selected group of molecules to natural ligands. Individual work on solving problems.
    6. Statistical methods, QSAR, CADD methods and CAMD.
    Practical part: Presentation of the program to calculate the QSAR, CADD and CAMD (presentation and practical demonstration). Individual work on solving problems.
    7. Finishing the seminary works, presentation of results in the form of protocols.
    8. Evaluation of the seminary works. The granting of credits. (2 hours)
Language of instruction
English
Further comments (probably available only in Czech)
The course can also be completed outside the examination period.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/pharm/spring2020/FAMM1_12