Protein Structure Analysis

Exploring the Protein Data Bank
6 Topics
Searching for a Structure via the Protein Data Bank by PDB ID
Searching for a Structure via the Protein Data Bank by Sequence
The PDB file
Downloading the Structure
Searching for a Structure via Uniprot by Sequence
Searching for a Structure via the EBI Sequence Similarity Search
Visualizing a Structure
15 Topics
Installing Python and PovRay
Working with YASARA
Scene styles
Showing and Hiding Residues
Showing and Hiding Secondary Structure
Labels
Colours
Saving All the Beautiful Work
Creating High Quality Images
Distances
Hydrogen Bonds
Surfaces
Molecular Graphics Exercise
More Coloring
Conclusion
Comparing Structures
3 Topics
Structural Comparison and RMSD
Aligning Multiple Structures Using YASARA
Conclusion
Predicting the Effect of a Mutation on a Protein Structure
6 Topics
Introduction to Mutations in Proteins
P53 as Example Protein
FoldX Energies
Minimizing the Structure with FoldX
How to Analyze a Mutation
Conclusion
Predicting a Protein Structure – Homology Modelling
8 Topics
Introduction to Homology Modelling
Main Ingredients for Homology Modelling
Building the Homology Model with Swiss Model
Aligning Target, Template Sequence & Template Selection
Swiss Model: The Template Selection
Swiss Model: Model Building & Visualisation
Conclusion
Analyse the template suggestion from SWISS-Model
Protein-ligand Interaction – From Small Molecule to Protein
5 Topics
Introduction
Exploring the Structure of a Nanobody-Stabilized Active State of the β2 Adrenoceptor – the Ligand
Exploring the Structure of a Nanobody-Stabilized Active State of the β2 Adrenoceptor – the Nanobody
Comparing the Active and the Inactive Conformation of the β2 Adrenoceptor
Conclusion
Introduction
36 Topics
Sequences and Structures
Amino Acids and Peptide Structure
The Structure-Function Connection
Databases
X-Ray Crystallography – Technical Setup
X-Ray Crystallography – From Diffraction Pattern to Atomic Model
The Protein Databank
Exercise 1: Search the PDB
PDB File Format
Occupancy
Related Websites
High-Resolution NMR Spectrometry – Principles
High-Resolution NMR Spectroscopy – Nuclear Overhauser Effect
High-Resolution NMR Spectroscopy
Other Methods
Related Websites
Assessing Structure Quality
Molecular Graphics Software
YASARA
Exercise 2: Show a Structure
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Introduction

Protein Structure Analysis Introduction
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