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Programme
The course will cover through a combination of lectures and hands-on tutorials.
PDB history
Day 1
Target to Domain selection
Is my Target a complex requiring co-expression ?
Morning lectures
1. 09:00 - 09:10 Introduction Kim Henrick,
talk
2. 09:10 - 09:50 Target Optimisation Utility Geoff Barton and Ian Overton,
tutorial
paper
3. 09:50 - 10:30 Co_expression - Misha Kapushesky ,
Tutorial, talk
4. 10:50 - 11:30 InterPro - Sandra Orchard talk,
Tutorial,
paper
5. 11:30 - 12:10 Pfam - Rob Finn,
talk, Tutorial
paper
Afternoon Tutorials 13:30 - 17:00
Taro, ArrayExpress, InterPro, Pfam
Day 2
Introduction to PiMS Information management System
Lectures and use of PiMS on Construct design
Lectures and use of PiMS in Expression
Lectures and use of PiMS in Purification
Lectures on Practical Crystallisation Experience and Suitability of Screens and use of xtalPiMS
Morning Lectures
1. 09:00 - 09:40 PiMS Robert Esnouf, Talk
2. 09:40 - 10:20 PiMS demo's lectures Chris Morris,
Talk, Jon Diprose
talk, Anne Pajon
Talk
3. 10:50 - 11:30 xtalPiMS Ian Berry, Talk
4. 11:30 - 12:10 Xtrack Mark Harris, demo,
paper
Afternoon Tutorials 13:30 - 17:00
PiMS, xtalPiMS, Xtrack Tutorial files (Clone 3+4 screen gel 1 111206.tif, master_plate_pcr_products_051206.tif, pcr screen miniprep pOPINEbsh construts 121206.tif, PCRGel.jpg, SDSPAGE BSH small scale whole cell.tif, tags.txt, Tutorial_TrialExpression.csv )
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Day 3
Ligand Dictionary
Validation of Protein Structures
Validation of Ligands
Checking Ligand environment with the PDB
Morning Lectures
1. 09:00 - 09:40 Validation of ligands - Gerard Kleywegt,
Talk, Tutorial,
EDS, HIC-UP, ValLigURL,
Validation, EDS paper,
Ligand paper, Valligurl paper,
Limitations paper
2. 09:40 - 10:20 RCSB and Ligands - John Westbrook, Tutorial,
ligand-expo
Talk
3. 10:50 - 11:30 PDBe ligands - Dimitris Dimitropoulos,
talk,
Tutorial1,
Tutorial2,
paper
4. 11:30 - 12:10 MSDmotif - Adel Golovin,
talk,
tutorial
Afternoon Tutorials 13:30 - 17:00
Ligand Depot, ValLigURL, MSDchem MSDmotif
Dinner at the College map
Day 4
Structure to Function
1. 09:00 - 09:40 Terri Attwood , Talk,
Tutorial
paper
2. 09:40 - 10:20 SSM and PISA Eugene Krissinel, Pisa-talk,
SSM-talk
3. 10:50 - 11:30 Functional annotation of proteins through structural data - Roman Laskowski tutorial
paper
4. 11:30 - 12:10 MSDtemlate,
Tutorial Tom Oldfield
Afternoon Tutorials 13:30 - 17:00
Day 5
Structure comparisons
Searching Structure Databases
1. 09:00 - 09:40 PSI KnowledgeBase - Helen Berman, Tutorial, talk
2. 09:40 - 10:20 STRAP Workbench Christoph Gille, talk
3. 10:50 - 11:30 PDBj Search tools Haruki Nakamura, Tutorial
4. 11:30 - 12:10 Exploiting Domain Family Classifications for Functional Annotation of Protein Structures - Christine Orengo
talk,
paper
Afternoon Tutorials 13:30 - 16:00
5. 16:00 - 16:40 Kim Henrick
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