Virtual course

Structural bioinformatics (Virtual)

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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.

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.

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 support 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.

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 wet-lab 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.

Prerequisites 

A working knowledge of the Linux operating system and ability to use the command line would be a benefit but is not mandatory. 

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
  • Explore protein-complex modeling approaches
Course content

During this course you will learn about: 

Trainers

David Armstrong
EMBL-EBI, UK
Christine Orengo
University College London, UK
Piraveen Gopalasingam
EMBL-EBI, UK
Gerard Kleywegt
EMBL-EBI, UK
Rossana Zaru
EMBL-EBI, UK
Fabio Madeira
EMBL-EBI, UK
Alexandre Bonvin
Utrecht University
Michael Sternberg
Imperial College London, UK
Anna Gaulton
EMBL-EBI, UK
Typhaine Paysan-Lafosse
EMBL-EBI, UK
Osman Salih
EMBL-EBI, UK

Programme

Day 1 - Monday 23rd Nov
09:00 - 10:00 Live: Welcome presentation & Meet the Delegates  Piv Gopalasingam, David Armstrong and Meredith Willmott
10:00 - 10:45  Live Keynote: Structural informatics: Past and Future Janet Thornton
10:45 - 11:00  Live: Q&A  Janet Thornton
11:00 - 11:30  Break   
11:30 - 12:30 Live: Introduction to structural biology data Gerard Kleywegt
12:30 - 13:30  Live: Flash talks 1-7  All
13:30 - 14:30  Break   
14:30 - 15:30 Live: Flash talks 7-14 All
15:30 End of day   
Own time  Sequences: Alignments and Annotation homework  Rossana Zaru and Fabio Madeira
Day 2 - Tuesday 24th Nov
08:45 - 09:00  Live: Morning social bingo  Piv Gopalasingam and Meredith Willmott
09:00 - 09:30 Live: Sequences- Alignments and Annotation  Rossana Zaru and Fabio Madeira
09:30 - 10:45  Sequence classification: InterPro & HMMER Typhaine Paysan-Lafosse
10:45 - 11:00  Live: Q&A  Typhaine Paysan-Lafosse
11:00 - 11:30  Break   
11:30 - 13:00  Sequence classification: InterPro & HMMER (hands-on) Typhaine Paysan-Lafosse
13:00 - 14:00  Break   
14:00 - 15:00 Live: CATH DB - Protein folds and structural family resources Ian Sillitoe
15:00 - 15:30  Live: Q&A and practical Ian Sillitoe
15:30 - 16:00  Break   
16:00 - 17:00  Live: Flash talks 14 - 21 All
17:00 - 17:30  Live: Daily recap session  All
Day 3 - Wednesday 25th Nov
08:45 - 09:00  Live: Morning coffee chat  Piv Gopalasingam and Meredith Willmott
09:00 - 09:45 PDBe: Finding, validating and visualising structural data David Armstrong 
09:45 - 11:00 Live: PDBe: Finding, validating and visualising structural data, Q&A and practical David Armstrong and Deborah Harrus
11:00 - 11:30  Break   
11:30 - 12:00 PDBe tools - in-depth analysis of protein structure David Armstrong
12:00 – 13:00 Live: PDBe tools - in-depth analysis of protein structure, Q&A and practical David Armstrong and Deborah Harrus
13:00 - 14:00  Break   
14:00 - 15:00 EM data and protein complexes Osman Salih
15:00 - 15:30 Live: EM data and protein complexes Q&A and practical Osman Salih
15:30 - 17:00  Live: Flash talk 21- 30  All
17:00 - 17:30  Live:  Daily recap session David Armstrong, Piv Gopalasingam
17:30 End of day   
Day 4 - Thursday 26th Nov 
09:00 - 11:00  Live: Protein structure prediction - Phyre2 Michael Sternberg
11:00 - 11:30 Break  
11:30 - 13:00 Exploring protein docking with HADDOCK – pre-recorded lectures (two parts) Alexandre Bonvin
13:00 - 14:00  Break  
14:00 - 15:45 Live: Q&A session and computer practical - Exploring protein docking with HADDOCK Bonvin group
15:45 - 16:00  Break   
16:00 - 16:45  Live: Exploring protein docking with HADDOCK – interactive multiple choice lecture Alexandre Bonvin
16:45 - 17:15 Live: interface prediction and binding affinity prediction – analysing the docked models Bonvin group
17:15 End of day   
Day 5- Friday 27th Nov
08:45 - 09:00  Live: Morning coffee chat  Piv Gopalasingam and Meredith Willmott
09:00 - 09:30  PDBe-KB: Aggregated views of protein structure data David Armstrong
09:30 - 11:00 Live: PDBe-KB: Aggregated views of protein structure data, Q&A and practical David Armstrong / PDBe team
11:00 - 11:30  Break & Group Photo   
11:30 - 12:15 Ligand structural biology with ChEMBL Anna Gaulton / ChEMBL team
12:15 - 13:00  Ligand structural biology with ChEMBL Anna Gaulton / ChEMBL team
13:00 - 13:45 Break  
13:45 - 14:30  Live: Keynote Andrea Thorn
14:30 - 14:45  Live: Q&A  Andrea Thorn
14:45 - 15:15  Live: Course wrap-up and close David Armstrong and Piv Gopalasingam

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 02nd October 2020. 

Incomplete applications will not be considered.

All participants are expected to virtually present a poster during the course. We expect the posters to provide other delegates and trainers with information on your research and will act as a talking point. They should give an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing. When preparing the poster keep in mind that other participants will view it on a computer screen. make it concise, clear, and avoid small images. Further information regarding poster presentations will be provided after the deadline. 

This course has ended

23 - 27 November 2020
£200
Contact
Meredith Willmott

Organisers
  • Piraveen Gopalasingam
    EMBL-EBI, UK
  • David Armstrong
    EMBL-EBI, UK
  • Gerard Kleywegt
    EMBL-EBI, UK
  • Christine Orengo
    University College London, UK
  • Typhaine Paysan-Lafosse
    EMBL-EBI, UK

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