Inhalt
[ 675CHEMCCM17 ] Module Computational Chemistry and Molecular Modelling of Biomolecules





Workload 
Mode of examination 
Education level 
Study areas 
Responsible person 
Coordinating university 
4 ECTS 
Accumulative module examination 
B3  Bachelor's programme 3. year 
^{(*)}Bioinformatik 
Rüdiger Ettrich 
USB Budweis 



Detailed information 
Original study plan 
Bachelor's programme Bioinformatics 2017W 
Objectives 
The lectures are concerned with the subject of theoretical research of the structure, function and dynamics of molecules. Students will become familiar with the following topics: various computer representations of molecular structures, searching in structural databases, the acquisition of protein structural parameters, a brief overview of structurebased methods of energy computation, homology modelling and energy minimisationbased modelling, molecular dynamics, proteinligand interactions, prediction of protein structure and docking of ligands. The course also includes practical exercises concerning visualisation, modification and structure based computations on real molecular systems. Recommended literature, demonstration and application software will be available during the course.

Subject 
 MK1. Computer representations of molecular structure, techniques of visualization and modification of molecular structures, structural formats
 MK2. Structural databases of inorganic and organic molecules and biomolecules (proteins, nucleic acids and their complexes), overview of experimental methods for acquisition of molecular structure, complex search in structural databases
 RE3. Protein structure: dominant effects during the process of protein folding, geometrical parameters of polypeptide chain
 RE4. Sequential analysis: sequence alignment, dynamic programming by use of NeedlemanWunsch and SmithWaterman algorithms, substitution matrix.
 RE5. Prediction of protein structure and function
 RE6. Verification of structural parameters, stereochemistry of bio(macro)molecules, verification of folding.
 MK7. Energy modelling: Empirical models (force field method). Functional of potential energy, parameters, application, advantages and limitations.
 MK8. Energy modelling: Quantum chemical (QCH) models, approximation levels, numerical computations applied in solution of Schroedinger equation for multielectron systém like nonhydrogen atoms and molecules, limits of a QCH method.
 MK9: Application of quantumchemical methods for a computation of molecular and atomic features (atomic and molecular orbitals, electron density, charges, dipol and transition moments), optical and NMR spectra. Matrix method for the computation of multimer excitation states. Computations for systems in solvent environment. Statistical termodynamics (enthalpy of formation, entropy, Gibbs energy, etc.), computation of energy released in chemical reactions. Transition state searching, chemical kinetics.
 MK10. Potential energy as a hypersurface, its features, fysicalchemical interpretation of stationary points of hypersurface  local minimas and maximas, first and higher order saddle points. Energy minimisation: nonderivative methods, derivative methods  steepest descent method, conjugate gradient, Monte Carlo, etc.
 RE11. Comparable modelling: methods of space restriction, probability density function (PDF), space limitations. Fragment methods, root mean square deviation, structural frame, library of rotamers.
 RE12. Molecular dynamics: numerical integration, Verlet algorithm, force fields, water models, periodicity in water box, particle MeshEwalds, restriction of rotational and vibrational modes.
 RE13. Docking of ligands: Autodock, flexibilerigid, genetic algorithms, MonteCarlo simulated annealing




Subordinated subjects, modules and lectures 


