[ 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 structure-based methods of energy computation, homology modelling and energy minimisation-based modelling, molecular dynamics, protein-ligand 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.
  1. MK1. Computer representations of molecular structure, techniques of visualization and modification of molecular structures, structural formats
  2. 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
  3. RE3. Protein structure: dominant effects during the process of protein folding, geometrical parameters of polypeptide chain
  4. RE4. Sequential analysis: sequence alignment, dynamic programming by use of Needleman-Wunsch and Smith-Waterman algorithms, substitution matrix.
  5. RE5. Prediction of protein structure and function
  6. RE6. Verification of structural parameters, stereochemistry of bio(macro)molecules, verification of folding.
  7. MK7. Energy modelling: Empirical models (force field method). Functional of potential energy, parameters, application, advantages and limitations.
  8. 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.
  9. MK9: Application of quantum-chemical 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.
  10. MK10. Potential energy as a hypersurface, its features, fysical-chemical interpretation of stationary points of hypersurface - local minimas and maximas, first and higher order saddle points. Energy minimisation: non-derivative methods, derivative methods - steepest descent method, conjugate gradient, Monte Carlo, etc.
  11. RE11. Comparable modelling: methods of space restriction, probability density function (PDF), space limitations. Fragment methods, root mean square deviation, structural frame, library of rotamers.
  12. RE12. Molecular dynamics: numerical integration, Verlet algorithm, force fields, water models, periodicity in water box, particle Mesh-Ewalds, restriction of rotational and vibrational modes.
  13. RE13. Docking of ligands: Autodock, flexibile-rigid, genetic algorithms, Monte-Carlo simulated annealing
Subordinated subjects, modules and lectures