An introduction to the EBI's protein 3D structure databases and services

18-19 April 2007

Dear Friends,

The EBI will host an Industry Workshop ‘an introduction to the EBI's protein 3D structure databases and services’ on Wednesday 18th and Thursday 19th April 2007 at Hinxton, Cambridge. The Scientific Coordinators are Jawahar Swaminathan, Sameer Velankar and Roman Laskowski (EMBL-EBI).

The purpose of this workshop is to provide an introduction to the EBI's protein 3D structure databases and services. Participants will be shown how to get the best out of the Macromolecular Structure Database (MSD) and other services. The MSD is a partner in the worldwide Protein Data Bank (wwPDB) and is one of the 4 sites around the world that accept primary structure data from experimental biologists. The MSD also has a comprehensive relational database of 3D structures of biological molecules that is freely accessible by WWW-based tools for search, analysis and visualization. The MSD has a range of services from simple query engines to complex data analysis tools.

The workshop is intended for bioinformaticians supporting structural studies and molecular and structural biologists who wish to learn more about the services and technologies available at the EBI for the analysis of protein structure. It will consist of a mixture of talks and hands-on practical sessions. At the end of the workshop it is hoped that the participants will be able to use the EBI structural databases effectively and efficiently for their own research.

The search interfaces that will be covered in the workshop include:

MSDpro and MSDlite : simple and complex general queries.
MSDchem : searches covering all ligands in the PDB.
MSDsite : protein active sites, including bound ligands and their environments.
MSDfold : fold-matching via secondary structure alignment.
MSDpisa : Protein Interfaces, Surfaces and Assemblies (PISA).

Also covered will be an introduction to the AstexViewer@MSD: a sophisticated, intuitive and powerful molecular graphics viewer and visualization program to view and analyse the results from the above searches.

In addition to the above MSD services we will describe the following:

PDBsum : pictorial structural analyses of all 3D structures.
ProFunc : prediction of protein function from sequence and 3D structure.
SAS : Sequences Annotated by Structure (SAS).
CSA : the Catalytic Site Atlas.

The venue will be the James Watson and Rosalind Franklin Pavilions at the Wellcome Trust Conference Centre in Hinxton, Cambridge.

Please contact Liz Ford - ford@ebi.ac.uk - if you would like to register for this workshop.

Preliminary agenda:

Time	Agenda
April 18th 2007
09.00	Coffee and Registration
09.30	Session 1 - Introduction and data quality assessment
	Introduction to Structural Databases at the EBI
	Analysis of Structure using MSDvalidate and MSDtemplate Tutorials
12.30	Lunch
	Session 2 - Structure Analysis@MSD
	MSDlite and MSDfold: Simple search interfaces
	MSDPisa - Analysis of protein interfaces, surfaces and assemblies
	MSDfold - Analysis of protein fold using secondary structure alignments
	Tutorials
17.30	Finish
18.15	Depart for Workshop dinner
April 19th 2007
09.30	Session 3 - Research Services at EBI
	PDBsum : pictorial structural analyses of all 3D structures
	ProFunc : prediction of protein function from sequence and 3D structure
	SAS : Sequences Annotated by Structure (SAS)
	CSA : the Catalytic Site Atlas
	Tutorials
12.30	Lunch
	Session 4 - Other MSD services
	MSDchem: Ligand chemistry database
	MSDsite/MSDmotif: Ligand environment and binding site database and database of small structural motifs
	Tutorials and Conclusion
17.30	End