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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

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:

  • 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:

  • 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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