Structural biology, determining the three-dimensional shapes of biomacromolecules and their complexes, can tell us a lot about how these molecules function and the roles they play within a cell. Data derived from structure determination experiments enables life-science researchers to address a wide variety of questions. 2021 marks 50 years of the Protein Data Bank (PDB), the single worldwide archive of experimental biomacromolecular structures, highlighting the depth of knowledge available for understanding molecular structure and function.

This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts. The course content will also cover predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds. There will also be a short session covering the new AI-predicted protein structures database, AlphaFold DB.

This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures, and tutorials with live support. We will be using Zoom to run the live stream sessions (all fully password protected with automated English closed captioning and transcription) with support and networking opportunities provided by Slack. In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week. There will also be networking and short social activities throughout the course and efforts will be made to make these accessible at different time zones across the week.

Selected participants will be sent materials prior to the course. These might include pre-recorded talks and required reading or online training that will be essential to fully understand the course.

Who is this course for?

This course is aimed at scientists generating structural data or scientists utilising structural data in their analysis and/or interpretation. No previous experience in the field of structural bioinformatics is required, however a basic knowledge of protein structure would be of benefit.

What will I learn?

Learning outcomes

After this course you should be able to: 

• Access and browse a range of structural data repositories
• Determine whether appropriate structural information exists about a given small molecule, macromolecule or complex, applying available structure-quality information
• Build a structural model for a protein which has a structurally characterised relative and evaluate its quality
• Predict the function of a protein-based on sequence and structure data, and navigate & assess AI-predicted protein structures.
• Explore protein-complex modeling approaches

Course content

During this course you will learn about: 

• Public repositories of structural data: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), and tools to search and analyse information in these repositories from PDBe (Protein Data Bank in Europe) including PDBe-KB
• UniProt and basic Sequence alignment tools
• Protein structure analysis and classification: HMMER, InterPro, Pfam, CATH, PDBeFold, PDBePISA
• Protein structure prediction and docking: PHYRE2 and HADDOCK
• Structure validation and assessment tools and strategies
• Tools and resources for drug discovery: ChEMBL
• AI-predicted protein structures Database AlphaFoldDB

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form providing answers as directed
• Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography
  • work history
  • current research interests
• Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by midnight on Friday 09 July 2021. 

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 23 July 2021. If you have any questions regarding the application process please contact Meredith Willmott (meredith@ebi.ac.uk).