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Last update: T_FUUK (23.05.2006)
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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). |
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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. |
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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 |
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Last update: IBARVIK/MFF.CUNI.CZ (16.05.2008)
Lectures and practical excercises in computer lab. |
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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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