| Course title | Molecular Modelling |
|---|---|
| Course code | KFC/MOM |
| Organizational form of instruction | Lecture |
| Level of course | Bachelor |
| Year of study | 1 |
| Semester | Winter |
| Number of ECTS credits | 3 |
| Language of instruction | Czech, English |
| Status of course | Compulsory, Optional |
| Form of instruction | Face-to-face |
| Work placements | This is not an internship |
| Recommended optional programme components | None |
| Course availability | The course is available to visiting students |
| Lecturer(s) |
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| Course content |
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The lecture is focused on empirical methods and non-empirical are concerned marginally. 1. molecular coordinates ans topology 2. principles of molecular mechanics, harmonic approximation, torzional terms, noncovalent interaction and its description by empirical potencial, parc. charges, RESP, Ewald summ., vdW interaction, LJ potencial, cutoff, parametrization 3. common force fields and their limitations (AMBER, CHARMM, OPLS-AA etc.) 4. united atoms, coarse grained models, CGFF-MARTINI 5. classical molecular dynamics, PBC, thermostat, barostat, conditions, simulation protocols, analysis - evolution RMSD, Rg; essencial dynamics 6. water models, explicit and implicit (PB, GB) 7. enzyme and RNA catalysis, definition of catalytic effect, sources of catalysis, RNA and DNA enzymes, hybrid methods QM/MM 8. drug design, drug tests and evaluation, CADD, molecular docking, scoring function, COMFA 9. protein and NA folding 10. examples
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| Learning activities and teaching methods |
Monologic Lecture(Interpretation, Training)
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| Learning outcomes |
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This lecture provides knowledge concerning molecular modeling; from theory to applications.
ability to describe and recognize fundamental procedures and methods for the molecular modelling |
| Prerequisites |
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unspecified
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| Assessment methods and criteria |
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Oral exam
Student must be able to discuss two given topics. |
| Recommended literature |
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| Study plans that include the course |
| Faculty | Study plan (Version) | Category of Branch/Specialization | Recommended semester | |
|---|---|---|---|---|
| Faculty: Faculty of Science | Study plan (Version): Experimental Biology of Plants (2021) | Category: Biology courses | 1 | Recommended year of study:1, Recommended semester: Winter |
| Faculty: Faculty of Science | Study plan (Version): Biophysics - Specialization in Molecular Biophysics (2024) | Category: Physics courses | 3 | Recommended year of study:3, Recommended semester: Winter |