Monday 20th September - Shrubsole
Room |
| 9:00-9:05 |
Welcome: Dr Kim Henrick (EBI) |
| 9:05-9-40 |
An overview of the RCSB Protein Data Bank:
Dr. Helen M. Berman RCSB Protein Data Bank Rutgers,
The State University of New Jersey
A description of the resources for data deposition, validation
and query offered by the RCSB PDB will be given. |
| 9:40-10:20 |
Crystals, Symmetry and Protein Assemblies:
Dr Kim Henrick (EBI) |
| 10:20-11:00 |
Protein-DNA interactions: Dr Sue
Jones
Protein-DNA Interactions: analysis and predictions |
| 11:00-11:30 |
Coffee Break |
| 11:30-12:10 |
Using the ‘Thornton-Group’ WWW Database
Services for Structural Research: Dr Roman
Laskowski (EBI) |
| 12:10-12:50 |
Quaternary Structure Inference of Proteins from
their Crystals: Dr Hannes Ponstingl (EBI)
Protein-Protein Interactions: The basic principles which
determine the strength and geometry of protein-protein
complexes by Patch Analysis and other methods. |
| 12:50-14:00 |
Lunch Break |
| 14:00-14:40 |
Validation of protein structures ... Or: just
because it was published in Nature, doesn't mean it's
true !: Dr. Gerard Kleywegt (Uppsala University,
Sweden) |
| 14:40-15:20 |
3D databases and data warehouse technology:
Dr Phil McNeil (EBI) |
| 15:20-16:00 |
Clustering of 3D structures and representative
sets: Dr Thomas Oldfield (EBI) |
| 16:00-16:30 |
Coffee Break |
| 16:30-17:10 |
Sequences and 3D structures (Integration of
3D data and sequence databases): Dr Sameer
Velankar (EBI) |
| 17:10-17:50 |
Structure analysis: Professor
Janet Thornton (EBI) |
| 18:30 |
Welcome Dinner |
|
Tuesday 21st September
Participants are split into 2 groups |
| Morning session Group 1 - Creative
Room (tutorials) |
| 09:00-10:00 |
Searching 3D protein structures for conserved
DNA-binding motifs: Dr Sue Jones |
| 10:00-11:00 |
Using the 'Thornton-Group' WWW Database
Services for Structural Research: Dr
Roman Laskowski (EBI) (2hours)
CATRES, Catalytic Site Atlas (CSA), NetFunc, EC->PDB,
Pita - Protein Interfaces and Assemblies, Receptor
Structure and Function, Protein Side-Chain Interactions,
Practical: Structural Genomics |
| 11:00-11:30 |
Coffee Break |
| 11:30-12:30 |
Pfam and MEROPS: Robert Finn
(Sanger) |
| 12:30-13:30 |
Lunch Break |
Morning session Group 2 - Shrubsole
Room (lectures/demos) |
| 09:00-10:00 |
Protein Structure Classification and Genome
Annotation: Technologies and Insights from the CATH
Database: Professor Christine Orengo
(UCL, London) |
| 10:00-11:00 |
SCOP: Structural Classification of Proteins:
Dr Loredana Lo Conte (LMB, Cambridge) |
| 11:00-11:30 |
Coffee Break |
| 11:30-12:30 |
SSM fold characterization: Dr
Eugene Krissinel (EBI) |
| 12:30-13:30 |
Lunch Break |
Afternoon session Group 1 - Shrubsole
Room (lectures/demos) |
| 13:30-14:30 |
Protein Structure Classification and Genome
Annotation: Technologies and Insights from the CATH
Database: Professor Christine Orengo
(UCL, London) |
| 14:30-15:30 |
SCOP: Structural Classification of Proteins:
Dr Loredana Lo Conte (LMB, Cambridge) |
| 15:30-16:00 |
Coffee Break |
| 16:00-17:00 |
SSM fold characterization: Dr
Eugene Krissinel (EBI) |
| 18:30 |
Dinner |
Afternoon session Group 2 - Creative
Room (tutorials) |
| 13:30-14:30 |
Searching 3D protein structures for conserved
DNA-binding motifs: Dr Sue Jones |
| 14:30-15:30 |
Using the 'Thornton-Group' WWW Database
Services for Structural Research: Dr
Roman Laskowski (EBI) (2hours)
CATRES, Catalytic Site Atlas (CSA), NetFunc, EC->PDB,
Pita - Protein Interfaces and Assemblies, Receptor
Structure and Function, Protein Side-Chain Interactions,
Practical: Structural Genomics |
| 15:30-16:00 |
Coffee Break |
| 16:00-17:00 |
Pfam and MEROPS: Robert Finn
(Sanger) |
| 18:30 |
Dinner |
|
Wednesday 22nd September
Participants are split into 2 groups |
Morning session Group 1 - Creative
Room (tutorials) |
| 09:00-10:30 |
Validation of protein structures:
Dr Gerald Kleywegt (Uppsala) (90 min)
Just because it was published in Nature, doesn't mean
it's true! |
| 10:30-11:00 |
Coffee Break |
| 11:00-12:00 |
Learning about structures using the RCSB
PDB: Dr Wolfgang Bluhm (Univ of California)
(60 min) |
| 12:00-12:45 |
Evaluation of structure quality tutorial,
using RCSB tools: Ms Kyle Burkhardt (RCSB
PDB) |
| 12:45-13:45 |
Lunch Break |
Morning session Group 2 - Shrubsole
Room (lectures/demos) |
| 09:00-10:30 |
MSDchem, MSDlite, MSDpro, MSDsite J
Swaminathan / S Velankar / A Golovin (EBI) |
| 10:30-11:00 |
Coffee Break |
| 11:00-12:15 |
MSDmySQL, MSDmine D Dimitropoulos
/ H Bouselakis (EBI) |
| 12:15-12:45 |
Advanced AstexViewer integrated into 3D PDB
searches J Tate (EBI) |
| 12:45-13:45 |
Lunch Break |
Afternoon session Group 1 - Shrubsole
Room (lectures/demos) |
| 13:45-15:15 |
MSDchem, MSDlite, MSDpro, MSDsite J
Swaminathan / S Velankar / A Golovin (EBI) |
| 15:15-15:45 |
Coffee Break |
| 15:45-17:00 |
MSDmySQL, MSDmine D Dimitropoulos
/ H Bouselakis (EBI) |
| 17:00-17:30 |
Advanced AstexViewer integrated into 3D
PDB searches J Tate (EBI) |
| 18:30 |
Dinner |
Afternoon session Group 2 - Creative
Room (tutorials) |
| 13:45-15:15 |
Validation of protein structures:
Dr Gerald Kleywegt (Uppsala) (90 min)
Just because it was published in Nature, doesn't mean
it's true! |
| 15:15-15:45 |
Coffee Break |
| 15:45-16:45 |
Learning about structures using the RCSB
PDB: Dr Wolfgang Bluhm (Univ of California)
(60 min) |
| 16:45-17:30 |
Evaluation of structure quality tutorial,
using RCSB tools: Ms Kyle Burkhardt (RCSB
PDB) |
| 18:30 |
Dinner |
|
Thursday 23rd September
Participants are split into 2 groups |
Morning session Group 1 - Creative
Room (tutorials) |
| 09:00-10:00 |
Tutorials - using MSD Tools to solve Problems
(60 min) |
| 10:00-11:00 |
Tutorials - Database replication and use
on your Desktop (60 min)
MSDmySQL and MSDmine |
| 11:00-11:30 |
Coffee Break |
| 11:30-13:00 |
Tutorials - Scripting languages + data mining
Dr Jaime Prilusky (Weizmann Institute, Israel)
(90 min) |
| 13:00-14:00 |
Lunch Break |
Morning session Group 2 - Shrubsole
Room (lectures/demos) |
| 09:00-10:00 |
What is visualisation and how are complex
data represented? Prof Bob Spence (Imperial
College, London) |
| 10:00-11:00 |
Small Structural and Sequence Motifs:
Dr James Milner-White (University of Glasgow) |
| 11:00-11:30 |
Coffee Break |
| 11:30-12:00 |
Visualisation data mining: Dr
Thomas Oldfield (EBI) |
| 12:00-13:00 |
More on Patterns: Kim Henrick (EBI) |
| 13:00-14:00 |
Lunch Break |
Afternoon session Group 1 - Shrubsole
Room (lectures/demos) |
| 14:00-15:00 |
What is visualisation and how are complex
data represented? Prof Bob Spence (Imperial
College, London) |
| 15:00-16:00 |
Small Structural and Sequence Motifs:
Dr James Milner-White (University of Glasgow) |
| 16:00-16:30 |
Coffee Break |
| 16:30-17:00 |
Visualisation data mining: Dr
Thomas Oldfield (EBI) |
| 17:00-18:00 |
More on Patterns: Kim Henrick (EBI) |
| 18:30 |
Dinner |
Afternoon session Group 2 - Creative
Room (tutorials) |
| 14:00-15:30 |
Tutorials - Scripting languages + data mining
Dr Jaime Prilusky (Weizmann Institute, Israel)
(90 min) |
| 15:30-16:00 |
Tutorials - Database replication and use
on your Desktop
MSDmySQL and MSDmine |
| 16:00-16:30 |
Coffee Break |
| 16:30-17:00 |
Tutorials - Database replication and use
on your Desktop
MSDmySQL and MSDmine |
| 17:00-18:00 |
Tutorials - using MSD Tools to solve Problems
(60 min) |
| 18:30 |
Dinner |
|
Friday 24th September - Shrubsole
Room |
| 9:00-9-40 |
Summary of 3D data and WWW current
scientific resources for 3D structure: Dr
Thomas Oldfield (EBI) |
| 9:40-10:20 |
Now you've seen the services - a word about
Conceptual basis for data analysis, problem solving and
critical thinking: Kim Henrick (EBI)
|
| 10:20-11:00 |
Data Interchange / API's Data Integration Problems
/ Query Interchange: Dr John Westbrook (RCSB)
|
| 11:00-11:30 |
Coffee Break |
| 11:30-12:10 |
Feedback - WrapUp: Chair - Dr Helen
Berman (RCSB) |
| 12:10 |
Lunch & Close |
Last Modified: 06 September, 2004 |
