Molecular modelling and computational structural biology 2

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.

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.

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