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Mon 28 Nov - Tue 29 Nov 2016
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Protein Structure Analysis

Mon 28 Nov - Tue 29 Nov 2016


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 find 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.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here

Understanding of the basics of protein structure is expected.


Number of sessions: 2

# Date Time Venue Trainers
1 Mon 28 Nov 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Alex Mitchell,  Sara El-Gebali,  David Armstrong,  Alice Clark
2 Tue 29 Nov 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ian Sillitoe,  Andrew Martin,  Lawrence Kelley
Topics covered

Bioinformatics, Data mining, Data retrieval, Data visualisation, Database search, Protein structure analysis


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.

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

Presentations, demonstrations and practicals


Day 1 Topics Speaker(s)
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
Registration fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

2 days


A number of times per year

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