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Course info
KFC / MOM
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Course description
Department/Unit / Abbreviation
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KFC
/
MOM
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Academic Year
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2024/2025
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Academic Year
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2024/2025
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Title
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Molecular Modelling
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Form of course completion
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Colloquium
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Form of course completion
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Colloquium
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Accredited / Credits
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Yes,
3
Cred.
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Type of completion
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-
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Type of completion
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-
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Time requirements
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Přednáška
2
[Hours/Week]
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Course credit prior to examination
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No
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Course credit prior to examination
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No
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Automatic acceptance of credit before examination
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No
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Included in study average
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NO
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Language of instruction
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Czech, English
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Occ/max
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Automatic acceptance of credit before examination
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No
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Summer semester
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0 / -
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0 / -
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0 / -
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Included in study average
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NO
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Winter semester
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0 / -
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0 / -
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0 / -
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Repeated registration
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NO
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Repeated registration
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NO
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Timetable
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Yes
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Semester taught
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Winter semester
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Semester taught
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Winter semester
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Minimum (B + C) students
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not determined
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Optional course |
Yes
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Optional course
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Yes
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Language of instruction
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Czech, English
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Internship duration
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0
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No. of hours of on-premise lessons |
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Evaluation scale |
S|N |
Periodicity |
každý rok
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Periodicita upřesnění |
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Fundamental theoretical course |
Yes
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Fundamental course |
No
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Fundamental theoretical course |
Yes
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Evaluation scale |
S|N |
Substituted course
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None
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Preclusive courses
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N/A
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Prerequisite courses
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N/A
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Informally recommended courses
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N/A
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Courses depending on this Course
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N/A
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Histogram of students' grades over the years:
Graphic PNG
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XLS
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Course objectives:
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This lecture provides knowledge concerning molecular modeling; from theory to applications.
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Requirements on student
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Student must be able to discuss two given topics.
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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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Activities
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Fields of study
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Guarantors and lecturers
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Literature
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Recommended:
Clark, T. A Handbook of Computational Chemistry. John Wiley & Sons, New York, 1985.
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Recommended:
Havlas Z. Metody a aplikace teoretické chemie,. ÚOCHB, Praha, 1997.
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Recommended:
Burket, U., Alinger, N. Molecular Mechanics. ACS, Washington 1982, 1982.
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On-line library catalogues
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Time requirements
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All forms of study
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Activities
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Time requirements for activity [h]
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Preparation for the Exam
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90
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Total
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90
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Prerequisites - other information about course preconditions |
- |
Competences acquired |
ability to describe and recognize fundamental procedures and methods for the molecular modelling
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Teaching methods |
- Monologic Lecture(Interpretation, Training)
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Assessment methods |
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