Protein Structure Analysis

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protein structure analysis

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Analyzing the protein structure of your protein-of-interest can be advantageous in multiple ways. It can help you discover regions which are good candidates to interact with other proteins. It can help you discover new domains. It can help with identifying differences with homologuous proteins and a lot more.

Contributors

Alexander Botzki, Joost Van Durme, Janick Mathys

Maintainers

Alexander Botzki

SOFTWARE & COURSE MATERIAL

Please download and install the software you can find at https://catalog.vib.be/apps/#/app/131

Other course material can be found at https://data.bits.vib.be/pub/trainingen/PSA/

REFERENCES

Switchlab: Home of FoldX plugin
More information about FoldX plugin and troubleshooting
Wikipedia: Wiki page about PDB
wiki page explaining information on PDB
YASARA developers: Working with YASARA
Movie tutorials on YASARA

Course Content

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Exploring the Protein Data Bank 6 Topics

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Lesson Content

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Searching for a Structure via the Protein Data Bank by PDB ID

Searching for a Structure via the Protein Data Bank by Sequence

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

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Installing Python and PovRay

Working with YASARA

Showing and Hiding Residues

Showing and Hiding Secondary Structure

Saving All the Beautiful Work

Creating High Quality Images

Molecular Graphics Exercise

Comparing Structures 3 Topics

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Structural Comparison and RMSD

Aligning Multiple Structures Using YASARA

Predicting the Effect of a Mutation on a Protein Structure 6 Topics

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Introduction to Mutations in Proteins

P53 as Example Protein

Minimizing the Structure with FoldX

How to Analyze a Mutation

Predicting a Protein Structure – Homology Modelling 8 Topics

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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

Analyse the template suggestion from SWISS-Model

Protein-ligand Interaction – From Small Molecule to Protein 5 Topics

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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

Introduction 36 Topics

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Sequences and Structures

Amino Acids and Peptide Structure

The Structure-Function Connection

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

Related Websites

High-Resolution NMR Spectrometry – Principles

High-Resolution NMR Spectroscopy – Nuclear Overhauser Effect

High-Resolution NMR Spectroscopy

Related Websites

Assessing Structure Quality

Molecular Graphics Software

Exercise 2: Show a Structure

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