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Course, academic year 2022/2023
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Computer Modelling of Biomolecules - NBCM316
Title: Počítačové modelování biomolekul
Guaranteed by: Institute of Physics of Charles University (32-FUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2020
Semester: both
E-Credits: 4
Hours per week, examination: 1/2, C+Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Teaching methods: full-time
Note: enabled for web enrollment
you can enroll for the course in winter and in summer semester
Guarantor: RNDr. Ivan Barvík, Ph.D.
RNDr. Vladimír Kopecký, Ph.D.
Annotation -
Last update: T_FUUK (23.05.2006)
Drug design, searching and visualization of biomolecular structures, sequence similarity searching against nucleic acids and protein databases, alignment of a sequence to be modeled with known structures, homology modeling, docking - the identification of the low-energy binding modes of a small molecule within the active site of a macromolecule, efficient algorithms to search the potential binding modes, molecular dynamics simulations for systems with hundreds to millions of particles, force field parametrization and topology, file creation for unusual molecular system, practical excercises.
Aim of the course -
Last update: IBARVIK/MFF.CUNI.CZ (16.05.2008)

Basics of computer modeling of biomolecules will be given. Students will learn how to perform molecular dynamics simulations of large biomolecular systems (see annotation and syllabus).

Course completion requirements -
Last update: RNDr. Ivan Barvík, Ph.D. (30.10.2019)

The credit is awarded on condition of at least 70% attendance.

In case of non-fulfillment, it is necessary to elaborate and present tasks from topics where absences occurred.

The condition for passing the exam is the elaboration of assigned project.

Literature -
Last update: prof. RNDr. Marek Procházka, Ph.D. (30.04.2019)

A. R. Leach: Molecular Modelling: Principles and Applications - Pearson Education Limited: Harlow, 2001, ISBN 0582382106

D. Frenkel, B. Smit: Understanding Molecular Simulations: From Algorithms to Applications - Academic Press: San Diego, 2001, ISBN 0122673514

Ch. Chipot, A. Pohorille: Free Energy Calculations: Theory and Applications in Chemistry and Biology - Springer-Verlag: Berlin Heidelberg, 2007, ISBN: 9783540384472

F. Jensen: Introduction to Computational Chemistry - John Wiley & Sons Ltd.: West Sussex, 2007, ISBN: 0470058048

Teaching methods -
Last update: IBARVIK/MFF.CUNI.CZ (16.05.2008)

Lectures and practical excercises in computer lab.

Syllabus -
Last update: T_FUUK (23.05.2006)

1) Databases: PDB (proteins), NDB (nucleic acids)

2) Homology modeling: Modeller, Consensus, Fasta

3) Docking: AutoDock, Dock

4) Molecular dynamics: NAMD (mindy)

5) Molecular dynamics: AMBER (sander, pmemd, nmode, leap, antechamber, ptraj)

6) Molecular dynamics: GROMACS, Yasara

7) Analysis: PTRAJ, Carnal, 3DNA, MDTool

8) Visualization: Chimera, VMD + Raster3d

9) Ab initio calculations: Gaussian

10) Ab initio calculations: Gamess, NBO5, WebMO

11) Visualization: Molden, ChemCraft, MolScript, gOpenMol, Molekel

12) Force field parametrization: RESP, Glycam

13) Available hardware: ČR MetaCentrum CoupledClusters LUNA Svět Juelich Barcelona

14) Grid solution for biomolecules.

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