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Protein Structure Analysis

Description

This course covers data resources and analytical approaches for the discovery and interpretation of biomacromolecular structures.

Day 1 focuses on public repositories of structural data (Protein Data Bank and Electron Microscopy Data Bank) and resources for protein analysis and classification (Pfam, InterPro and HMMER)

Day 2 covers how to retrieve information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools.

 

Trainers

Alex Mitchell, EMBL-EBI

Andrew Martin, UCL

David Armstrong, EMBL-EBI

Ian Sillitoe, UCL

Lawrence Kelley, Imperial College

Sara El-Gebali, EMBL-EBI

 

Audience and Prerequisites

  • Understanding of the basics of protein structure is expected.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals.

 

Syllabus, Tools and Resources

During this course you will learn about:

  • Differences between pairwise similarity and homology based approaches for annotating protein sequences
  • How to find, visualise and interpret macromolecular structures in the PDB and EMDB using our online tools.
  • How CATH provides information on protein sequence, structure and function
  • How protein modelling works, how to model your own proteins and when to trust the results.
  • An overview of approaches to mutation effect prediction and their performance and limitations.

 

Learning Objectives

After this course you should be able to:

  • Use HMMER, Pfam and InterPro to annotate protein sequences
  • Discover protein and nucleic acid structures related to your area of work and understand how this information could be used to further your own research
  • Scan a protein sequence against CATH and interpret the significance and biological meaning of results
  • Create your own protein models and analyse their features and assess their reliability
  • Use mutation prediction methods and evaluate their performance.

 

Links

Book Here

 

Timetable

Day 1
9:30 – 12:30 Lecture/practical: Using HMMER, Pfam and InterPro to provide functional and structural annotation of proteins Sara El-Gebali & Alex Mitchell
12:30-13:30 Lunch
13:30 – 17:30 Lecture/practical: Searching and understanding macromolecular structure at the Protein Data Bank in Europe and the Electron Microscopy DataBank. David Armstrong
Day 2
9:30 – 12:00 Lecture/practical: Using CATH to find information about the structure and function of your protein sequence Ian Sillitoe
12:00 - 13:00 Lunch
13:00 – 15:15 Lecture/practical: Homology modelling Lawrence Kelley
15:15 – 17:30 Lecture/practical: Impact of genetic variation on protein structure and function Andrew Martin
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