EMBO Practical Course on Computational Structural Biology - from data to structure to function

Date:

 Monday 7 Friday 11 April 2014

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£150

Registration closed

Overview

This course aims to teach computational aspects of protein structure determination, validation and analysis. It will cover the background of different structural biology techniques and provide hands-on experience in building a model from X-ray diffraction data. In addition, participants will learn how to critically assess the quality of data and models, and gain expertise in the integration and visualisation of data from different techniques, thus enabling the analysis of protein structure data for functional relationships. The importance of protein structure to drug discovery will also be illustrated with sessions dedicated to small-molecules, protein-ligand docking and model validation.

Audience

This course aims to teach computational aspects of protein structure determination, validation and analysis to PhD students and post-docs working on the collection and analysis of protein structure data. The course will be highly interactive and will include many practical sessions. Attendees are strongly encouraged to bring their own data and ideas of work to be addressed during these sessions.

Syllabus, tools and resources

During this course you will learn about:

  • Structural data repositories: Protein Data Bank, Electron Microscopy Data Bank
  • Tools for model building, refinement and homology modeling: WHATIF, AutoRickshaw, ARP/wARP, and other software
  • Tools and resources for drug discovery: ChEMBL, GOLD for protein-ligand docking, PDBeChem, PDBeMotif
  • Tools and resources for protein analysis and classification: Pfam, CATH, SCOP, InterPro, PDBeFold, ProFunc

Outcomes

After this course you should be able to:

  • Interpret, compare and integrate data obtained from different structural biology techniques 
  • Build a model from X-ray diffraction data
  • Access a range of structural data from leading public repositories
  • Critically assess the quality of data and models and select the most appropriate structures for your particular needs
  • Use a variety of analysis tools to identify structural similarities that can help identify protein function.

Programme

Time Topic Trainer
 
Monday 07 April 2014 – The wwPDB, structure determination and model building
09:00 - 09:30 Welcome and introduction to the EBI Tom Hancocks
09:30 - 11:00 Participant group discussions and expectations
11:00 - 11:30 Tea/coffee break  
11:30 - 12:15 Introduction to the Protein Data Bank (talk) Gerard Kleywegt
12:15 - 13:00 Background to protein structure and its determination (talk) Joana Maria Soares Pereira
13:00 - 14:00 Lunch  
14:00 - 15:30 Data collection and model building (practical) Joana Maria Soares Pereira
15:30 - 16:00 Tea/coffee break  
16:00 - 17:30 Searching and retrieving PDB structures (practical) Matthew Conroy
17:30 - 18:30 Discussion session Gerard Kleywegt 
19:00-21:00 Dinner at Hinxton Hall
Tuesday 08 April 2014 - Structure determination techniques, structure validation
09:00 - 10:30 EM data and how X-ray strauctures relate to EM maps Ardan Patwardhan
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 NMR data (practical) Aleksandras Gutmanas
12:30 - 13:00 Lunch  
13:00 - 14:00 Poster session  
14:00 - 15:00 Hybrid methods (talk) Marc A. Marti-Renom
15:00 - 15:30 Tea/coffee break  
15:30 - 17:30 Model validation (practical) John Berrisford
17:30 - 18:30 Discussion session Ardan Patwardhan
19:00 - 22:00 Dinner at Hinxton Hall  
Wednesday 09 April 2014 - Small molecules, drug discovery and chemoinformatics
09:00 - 10:00 Small molecule identification (practical) Joana Maria Soares Pereira
10:00 - 10:30 Tea/coffee break  
10:30 - 11:30 Chemistry and PDB (practical) Gary Battle
11:30 - 13:00 Drug discovery and ChEMBL (practical) John Overington
13:00 - 14:00 Lunch  
14:00 - 15:30 Protein-ligand docking (practical) Tjelvar Olsson
15:30 - 16:00 Coach to Cambridge  
16:00 - 19:30 Free time in Cambridge/Social Activity  
19:30 - 22:00 Course dinner at Cambridge College - (Return coach back to Hinxton will be provided)  
Thursday 10 April 2014 - Protein classification, structure analysis and homology modelling
09:00 - 10:30 Protein folds and families, CATH, SCOP and Pfam (practical) Christine Orengo
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Quaternary structure and fold comparison Gaurav Sahni
12:30 - 13:00 Lunch  
13:00 - 13:30 Poster session  
13:30 - 15:00 Homology modelling (practical) Hanka Venselaar
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Protein function prediction (practical) Roman Laskowski
17:00 - 18:30 Discussion session Christine Orengo
19:00 - 22:00 Dinner to Hinxton Hall  
Friday 11 April 2014 - Interactions, motifs, patterns, and function prediction
09:00 - 10:30 Sequence and structure based patterns (practical) Alex Mitchell
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Evolution and assembly of protein complexes Sarah Teichmann
12:00 - 13:30 Lunch  
13:30 - 15:00 SAXS data (practical) Dimitri Svergun
15:00 - 16:00 Discussion and feedback session Tom Hancocks
16:00 End of course