Macromolecular Structure Database Group The Roadshow - from deposition... to knowledge

In April 2003 the MSD Group released the first of a new suite of web-based search and retrieval interfaces for macromolecular structure research (see MSD Services). These services allow for complex query building, but retain exceptionally fast retrieval of data. The data is generated from our relational database of the entire PDB and integrated with databases such as UniProt, InterPro, SCOP, CATH, PFAM and others.

From August 2005 we will release new services, additional to those already available on the web and including MSDpisa, MSDmotif and MSDtemplate. MSDpisa (Protein Interfaces, Searches and Assemblies) is a new MSD web-service for online analysis of protein interfaces and quaternary structures. MSDmotif is a service for the interactive search and retrieval of three-dimensional motifs in protein structures. MSDtemplate is a discovery driven service for protein structure data analysis. In addition, we will release the next version of the cutting edge visualization tool, AstexViewT@MSD-EBI developed from the AstexViewerT (from Astex Technology Limited).

Roadshow & recent educational visits: 2004 - 2007:
Birkbeck College, LondonTraining day at Oxford University, Feb 2005
Imperial College, LondonSpeaker at BCA 2005
Biozentrum, Basel, SwitzerlandSpeaker at ACA 2005
UMIST (BCA 2004), ManchesterSpeaker at Swedish Structural Biology Conference
CSC, Helsinki, Finland IUCr, Florence
Turku Institute, Turku, Finland Industry Workshop, October 2005
Bilboa University, Bilboa, SpainDESY, Hamburg, November 2005
Cologne University, Cologne, GermanySW consortium, Bath, April 2006
Cambridge University, Cambridge Stanford University, San Francisco, US, June 2006
York University, York SDSC, San Diego, US, June 2006
Oxford University, Oxford VIB, Leuven, November 2006
EMBL-Hamburg, Hamburg, Germany Cambridge University Training Days, November 2006
EMBO Training Workshop, Sept 2004 Portsmouth University, November 2006
ISMB/ECCB, Vienna 2007Euromar 2007
MCCMB 2007 CMTPI 2007

Format of the Roadshow

Typical Version 1 (Half-day hands-on session of c.a. 4 hours incl. 15 min break)

  1. Overview presentation of the MSD activities including brief introduction to relational data base technologies (45mins)
  2. An introduction to the MSD web services including (60mins)
    1. The basic web front end to the oracle database and its use for related database links e.g. UniProtKB/Swissprot/MEDLINE
    2. The modified AstexViewer™ and its capabilities
    3. The drag&drop (Patent Pending) front end to the MSD Oracle database
    4. The protein-ligand search system
    5. The fold recognition search system
    6. The secondary structure element search system
    7. Residue Pattern searching
    8. A brief introduction to the other MSD services
    1. Validation server (to include the EDS service aspects to be built into the EBI systems later into the year)
    2. PQS server (being replaced by the Oracle system)
    3. Deposition systems
  3. A tutorial practical session (120 mins) for up to 30 desktop machines. This will start with a set of problem query examples and the tutors will be available to help with specific queries of interest from the participants.

The whole process can then be repeated in the afternoon to a different set of people.

Typical Version 2 ( A lecture session with no hands-on of c.a. 3 hours)

Similar to version 1 but without a tutorial room and the lectures will contain all the problem query examples as a demonstration by the tutors. Time will be allocated to query requests from the audience. More time can be spent on any of the following if required:

  1. the meaning of validation tests
  2. the background to data warehouse technology
  3. data cleaning aspects
  4. a particular MSD service from the above that would be of more interest to the audience.

Example Presentations & Demonstrations

PDF Files
PPT Files

Document mantained by: Gaurav Sahni