*Conducted in terms:*2020L, 2021L

*ECTS credits:*6

*Language:*Polish

*Organized by:*Faculty of Mathematics, Informatics, and Mechanics

# Molecular modelling and computational structural biology 2 1000-716MM2

From Born-Oppenheimer approximation to a mechanical model of (bio)molecular systems. Microscopic and mezoscopic interaction potentials. Hydrodynamic interactions. Determination of stable structual states - local and global energy minimization methods. Steepest descend and Newton-Raphson methods, operators allowing smoothing the energy hypersurface. Examples of stable strucures of nucleic acids and proteins. A, B and Z DNA. Protein folds. Structure comparison methods for proteins and nucleic acids. Homology of sequences and structures. Molecular motions - microscopic classical and quantum molecular dynamics, and mezoscopic Brownian Dynamics. Description of algoritms and stability analysis. Monte-Carlo methods and free-energy simulations. Thermodynamic perturbational approach. Computational alchemy. Physics and molecular evolution processes. Molecular folding mechanisms. Biomolecular recognition processes. Complex systems and biomolecular machines. Biomolecular machines and complex systems. From rate constants to signaling and regulation systems. Examples of oncogenic mutations and their influence on regulation processes.

## Main fields of studies for MISMaP

biology

physics

computer science

biotechnology

mathematics

## Mode

Blended learning

## Prerequisites (description)

## Course coordinators

## Learning outcomes

Teaching students mathematical and computational moledcular modeling methods, simulations of selected processes using molecular mechanics and dynamics methods, Monte-Carlo methods, and basics of systems theory. Lecture and excercises allow students modeling biomolecular systems and design of enzyme ihibitors - potential drugs.

## Assessment criteria

Credits for two exercises and the exam in a form of a test.

## Practical placement

Possible practices in the Institute of Experimental and Clinical Medicine PAS in Warsaw.

## Bibliography

1. D.W.Heermann, Podstawy symulacji komputerowych w fizyce, WNT, Warszawa, 1997.

2. Robert Kosiński, Wprowadzenie do mechaniki kwantowej i fizyki statystycznej, Oficyna Wydawnicza Politechniki Warszawskiej, Warszawa 2006.

3. L.Piela, Ideas of Quantum Chemistry, PWN, Warsaw, or another textbook in molecular quantum mechanics

4. P.O.J. Dcherer, S.F. Fischer, Theoretical Molecular Biophysics, Springer, Heidelberg, 2010 (ISBN 978-3-540-85609-2)

5. A.R.Leach, Molecular Modelling: Principles and Applications (2nd Edition), Prentice Hall; ISBN: 0582382106, 2001.

6. Materials to lectures http://kms.bioexploratorium.pl/

## Additional information

Additional information (*registration* calendar, class conductors,
*localization and schedules* of classes), might be available in the USOSweb system: