Moodle.UP

Topic

Lecture

Details

1

Introduction, Experimental methods for structure determination

X-ray, NMR, SAXS, Electron Microscopy, Spectroscopy  (CD, IR) and others

2

Principles of Protein Structures I

1D-2D-3D, Surface Calculation, Packing

3

Principles of Protein Structures II

Domains, 4D, Folds, Fold-DBs, Structure Comparison

4

The Protein Folding Problem

Underlying forces, properties of amino acids, lattice proteins, folding funnel

5

Molecular Dynamics Simulation

ab initio methods, Force fields, Molecular dynamics simulation

6

Energy minimization methods

Energy minimization, Monte Carlo, Simulated Annealing

7

Database derived potentials, Docking

Sippl Potential, Principles of protein docking, Small molecule docking

8

Statistics/Sequence-based Protein Structure Prediction

Secondary Structure Prediction, TM prediction, Unstructured regions

9

Statistics/Sequence-based protein structure prediction continued, Homology Modeling I

Principle of Homology Modeling, Loop modeling, Threading

10

AI in protein structure prediction & design

AlphaFold, ESMfold, embedding, protein design

11

RNA Structure Prediction I

RNA Sequence-Structure Relationships

12

RNA Structure Prediction II

RNA Sequence-Structure Relationships