Computational structural biology

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.

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Time Topic Trainer

Monday 07 April 2013 – The wwPDB, structure determination and model building
09:00 - 09:30 Welcome and introduction to the EBI Janet Thornton
09:30 - 11:00 Participant flash presentations
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) Victor Lamzin
13:00 - 14:00 Lunch
14:00 - 15:30 Data collection and model building (practical) Victor Lamzin
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 2013 - Structure determination techniques, structure validation
09:00 - 10:30 SAXS data (practical) Dimitri Svergun
10:30 - 11:00 Tea/coffee break
11:00 - 12:30 EM data and how X-ray structures relate to EM maps (practical) Ardan Patwardhan
12:30 - 13:30 Lunch
13:30 - 15:00 NMR data (practical) Aleksandras Gutmanas
15:00 - 15:30 Tea/coffee break
15:30 - 16:30 Hybrid methods (talk) Marc A. Marti-Renom
16:30 - 17:30 Model validation (practical) Swanand Gore
17:30 - 18:00 Discussion session Dimitri Svergun
18:00 - 20:00 Poster session
20:00 - 22:00 Dinner at Hinxton Hall
Wednesday 09 April 2013 - Small molecules, drug discovery and chemoinformatics
09:00 - 10:00 Small molecule identification (practical) Tim Wiegels
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) Susan Henderson
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 2013 - 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 (practical) Gaurav Sahni
12:30 - 13:30 Lunch
13:30 - 15:00 Homology modelling (practical) Gert Vriend
15:00 - 15:30 Tea/coffee break
15:30 - 17:00 Protein function prediction (practical) Roman Laskowski
17:00 - 18:00 Discussion session Christine Orengo
18:00 - 20:00 Poster session
20:00 - 22:00 Dinner to Hinxton Hall
Friday 11 April 2013 - 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 Protein-protein interactions and motifs (talk) Sarah Teichmann
12:00 - 13:30 Lunch
13:30 - 15:00 Protein-ligand interactions and binding motifs (practical) Sanchayita Sen
15:00 - 16:00 Discussion and feedback session Tom Hancocks
16:00 End of course

7 Apr - 11 Apr 2014
hinxston

meeting website