Inhalt

[ 863ABBCAMM15 ] Module Applications of Molecular Modelling

Versionsauswahl
Es ist eine neuere Version 2018W dieses Fachs/Moduls im Curriculum Master's programme Joint Master Programme Biological Chemistry 2018W vorhanden.
Workload Mode of examination Education level Study areas Responsible person Coordinating university
2 ECTS Accumulative module examination M2 - Master's programme 2. year (*)Biologische Chemie Norbert Müller USB Budweis
Detailed information
Original study plan Master's programme Joint Master Programme Biological Chemistry 2015W
Objectives This set of lectures gives an introduction to the theoretical study of structure, function and dynamics of biomolecules with a focus on proteins and nucleic acids. After a brief explanation of basic principles of quantum chemistry, the consequent lectures are focused on various computational methods ranging from ab initio approaches, semiempirical methods, empirical force fields, molecular dynamics, homology modeling to docking, combinatorial chemistry, QSAR methods and structure prediction. Hands-on exercises will give insight how to obtain and modify structure and properties of relative small molecules (tens of atoms) using ab initio methods as well as how to conduct computer experiments of larger systems (hundreds or thousands) of biological interest using classical molecular dynamics. Students become familiar with the UNIX operating system, visualization of biomolecules, molecular modeling and data analysis.
Subject 1. Introduction to quantum theory: Schrödinger equation and its approximations, valence bond theory, wave function.

2. Computational methods of quantum and theoretical chemistry: ab initio approaches, semiempirical methods, empirical force fields, molecular dynamics, homology modeling; commonly used programs in the computational chemistry.

3. Computational experiments and simulations: classical and ab initio molecular dynamics, Monte Carlo, calculations of statistical and thermodynamics values.

4. Intra- and intermolecular interactions in biomolecules.

5. Nucleic acids: structure and dynamics of nitrogenous bases and base pairs, simulations of large fragments (oligomers) of nucleic acids.

6. Proteins: structure and dynamics of amino acids, dominant effects during the process of protein folding, geometrical parameters of polypeptide chain, peptides, docking, combinatorial chemistry, QSAR methods.

7.UNIX operating system, basic commands, work with text editors.

8. Applications of quantum chemical programs (GAUSSIAN, TURBOMOLE), programs for empirical calculations (molecular mechanics and dynamics (AMBER, GROMACS, CHARMM).

9.Computer graphics: building of the molecule, vizualization of the results obtained by computational experiments.

10. Structural databases in chemistry and biology: Retrieving of structures, statistical methods, data sorting and handling.

Content of practicals: 1.UNIX operating system, basic commands, work with text editors.

2. Applications of quantum chemical programs (GAUSSIAN, TURBOMOLE), programs

3.Computer graphics: building of the molecule, vizualization of the results obtained by computational experiments.

4. MD , docking an QSAR and other simulations of biopolymers

Further information Recommended reading:

David Young: Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, 408 pp., 2001.

Frank Jensen: Introduction to Computational Chemistry, 2nd Edition, 620 pp., October 2006

Andrew Leach: Molecular Modelling: Principles and Applications, 744 pp., Pearson Education, 2001.

James B. Foresman: Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian

Corresponding lecture in collaboration with 863ABBCCCM15: Module Computational Chemistry and Modelling of Biomolecules (4 ECTS) equivalent to
863ABBCCOC12: Module Computational Chemistry (6 ECTS)
Subordinated subjects, modules and lectures