This course covers data resources and analytical approaches for the discovery and interpretation of biomacromolecular structures.
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.
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.
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.
|9:30 – 12:30||Lecture/practical: Using HMMER, Pfam and InterPro to provide functional and structural annotation of proteins||Sara El-Gebali & Alex Mitchell|
|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|
|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|