Hands-on training at EBI - EMBO Practical Course on Computational aspects of protein structure determination and analysis: from data to structure to function

Course Summary

Title: EMBO Practical Course on computational aspects of protein structure determination and analysis: from data to structure to function
Date: 6-10 September 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: James Watson, Rosemary Wilson
Admin Support: Alison Barker, Holly Foster
Registration Opens: 6 March 2010
Registration Deadline: 23 July 2010 - 12 noon (GMT)
Acceptance Notification Date: 30 July 2010 - 12 noon (GMT)

The course materials are now available to download. You will need a username and password to access these files. This is only available to people who attended the course (contact courses@ebi.ac.uk for details). Please take note of any materials licensing notices in these documents.

To download a zip folder of each day's course materials click on the relevant link:

Course Programme

Time	Topic
Day 0 - Sun 5 Sep 2010 - Arrivals at accomodation
Day 1 - Mon 6 Sep 2010 - Introduction, The wwPDB, Structure Determination and Model Building
09:00 - 09:30	Welcome and introduction to the EBI (Janet Thornton)
09:30 - 10:30	Introductory talk: "Background to protein structure and its determination" (Victor Lamzin and Santosh Panjikar)
10:30 - 11:00	Coffee Break
11:00 - 12:30	Talk and Practical: Introduction to the wwPDB and the PDBe. Practical searches of the wwPDB and extraction of data. Use of molecular graphics viewers. (Gerard Kleywegt, Gaurav Sahni, Matthew Conroy)
12:30 - 13:30	Talk and Demo session: "NMR data" (Wim Vranken)
13:30 - 15:00	Buffet lunch and poster session
15:00 - 15:45	Lecture: "Model building and automation" (Victor Lamzin and Santosh Panjikar)
15:45 - 16:45	Practical session: "Model building using AutoRickshaw, ARP/wARP, and other software" (Victor Lamzin and Santosh Panjikar)
16:45 - 17:00	Coffee Break
17:00 - 18:30	Practical session (continued): "Model building using AutoRickshaw, ARP/wARP, and other software" (Victor Lamzin and Santosh Panjikar)
18:30 - 18:45	Wrap up of day and questions (All trainers)
18:50	Buses depart to Cambridge. Evening dinner at hotel.
Day 2 - Tue 7 Sep 2010 - Further Structure Determination Techniques, Structure validation, and classifying folds and families
09:00 - 11:00	Talk and Practical exercise: "SAXS data" (Maxim Petoukhov)
11:00 - 11:30	Coffee break
11:30 - 12:30	Talk and demo: "EM data and how X-ray structures relate to EM maps" (Christoph Best)
12:30 - 13:30	Lunch
13:30 - 15:00	Talk and practical: "Model Validation" (Swanand Gore and Gaurav Sahni)
15:00 - 16:15	Talk and exercise: "Protein Folds and Families, CATH" (Christine Orengo)
16:15 - 16:45	Coffee Break
16:45 - 17:45	Talk/Demo: "Protein Folds and Families, Pfam" (Rob Finn)
17:45 - 18:30	Open panel discussion session: Structure determination, validation, the PDB and protein folds/families Questions on Days 1 and 2 (Victor Lamzin, Santosh Panjikar, Gerard Kleywegt, Gaurav Sahni, Matthew Conroy, Wim Vranken, Maxim Petoukhov, Christoph Best, Swanand Gore, Christine Orengo, Rob Finn)
18:40	Buses depart to Cambridge. Evening dinner at hotel.
Day 3 - Wed 8 Sep 2010 - Protein structure analysis (folds and assemblies), membrane proteins and homology modelling
09:00 - 11:00	Talk and Practical: "Quaternary structure and fold comparison - PDBeFold/PDBePisa" (Jawahar Swaminathan, Martyn Symmons)
11:00 - 11:30	Coffee break
11:30 - 12:45	Talk and Practical: Membrane protein structure data (Marialuisa Pellegrini-Calace)
12:45 - 13:30	Lunch
13:30 - 15:30	Talk and Practical Exercise: Homology Modelling (Gert Vriend)
15:40	Bus departs to Cambridge for punting trip (weather permitting)
16:00 - 17:00	Punting tour (weather permitting) followed by free time in Cambridge
19:30	Formal dinner at a Cambridge college
Day 4 - Thu 9 Sep 2010 - Motifs, Patterns, Active Sites and Function Prediction
09:00 - 11:00	Talk and Practical: "Structural Motifs - PDBeMotif" (Adel Golovin, Matthew Conroy, Sanchayita Sen)
11:00 - 11:30	Coffee break
11:30 - 12:30	Talk/Demo: "Enzymes and active sites: Macie" (Gemma Holliday)
12:30 - 14:00	Lunch and poster session
14:00 - 15:00	Talk/Demo: "Enzymes and active sites: Catalytic Site Atlas" (Nicholas Furnham)
15:00 - 15:30	Tea break
15:30 - 17:30	Lecture and practical session: "Protein function prediction" (Roman Laskowski, James Watson)
17:30 - 18:30	Open panel discussion session: Protein structure analysis, membrane proteins, homology modeling, motifs, patterns, active sites and function prediction. Participant discussion of wishes for the final day's sessions. (Jawahar Swaminathan, Martyn Symmons, Marialuisa Pellegrini-Calace, Gert Vriend, Adel Golovin, Matthew Conroy, Sanchayita Sen, Gemma Holliday, Nicholas Furnham, Roman Laskowski, James Watson)
18:40	Buses depart to Cambridge. Evening dinner at hotel.
Day 5 - Fri 10 Sep 2010 - Small molecules, drug discovery and chemoinformatics
09:00 - 10:30	Talk/Demo: "Protein interactions and small molecules: STRING and STITCH" (Michael Kuhn)
10:30 - 11:00	Coffee break
11:00 - 12:30	Lecture and practical session: "Chemistry in the PDBe using PDBeChem" (Jawahar Swaminathan, Sanchayita Sen)
12:30 - 13:30	Talk/Demo: "Chemoinformatics and ChEBI" (Christoph Steinbeck and Paula De Matos)
13:30 - 14:30	Lunch
14:30 - 15:30	Talk/Demo: "Drug discovery and ChEMBL" (John Overington)
15:30 - 16:00	Tea break
16:00 - 17:30	Practical session: "Small molecule docking" (John Overington)
17:30 - 18:00	Course closing comments and feedback session.

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