Structural Bioinformatics

Proteins and nucleic acids perform their functions because they can move, change conformations and recognize and bind other molecules. This course will introduce the computational tools, and some of the underlying theory, to study the structure and the dynamics of biomolecules. It will provide a comprehensive overview of basic and advanced topics in biomolecular simulations of proteins, small molecules, and nucleic acids, at different levels of resolution and in different environments. The course covers progresses in the development of atomistic, coarse-grained and quantum mechanical simulations and expand on methods for structure predictions based on statistical and evolutionary data and on hybrid methods that integrate structural biology techniques (Nuclear Magnetic Resonance, Small Angles X-Ray scattering, Cryo-electron microscopy) and computer simulations to increase the accuracy of computer simulations and experiments.
Each topic will be introduced theoretically and then learned hands-on using state-of-the-art software.
1. Molecular simulations approaches for proteins, small molecules, water, lipids, and nucleic acids (Force Fields, Classical Molecular Dynamics, Simple and Coarse grain models).
2. Quantum chemistry in action to study enzymes (Molecular simulations using quantum mechanics).
3. Protein Structure predictions (Secondary structure determination, Homology modeling, Protein structure prediction and design).
4. Methods for extracting equilibrium and kinetics properties (Conformational equilibrium and ligand binding).
5. Integrative Structural Biology (Modeling NMR, SAXS and Cryo-EM data to study protein structure and dynamics).
6. Analyzing, visualizing, and comparing biomolecular simulations.