Erice2010:workshop1

Databases of Protein Interactions

Here is some background information for workshop #1, Databases of Protein Interactions, led by Richard Bickerton from the University of Dundee.

Background

There is a dizzying array of diverse data resources regarding protein interactions, which vary widely in their scope, coverage and granularity. Rather than attempting to describe each of these in detail a few key resources will be highlighted. Two main themes will be resources that describe structural aspects of protein-protein interactions and databases of protein-small molecule interactions of use in drug discovery.

Aim

The aim of this workshop is to provide an introduction to the utility of a selection of resources and how they can be used to answer the kinds of questions a crystallographer may typically have e.g. What interaction partners does my protein have? What is the structural nature of these interactions? What features would suggest these interactions may be amenable to modulation by a small-molecule ligand? Along the way some fundamental aspects of protein-protein interactions will be considered, including some basic principles of molecular interactions, how interactions are represented and visualized, and what properties of protein interfaces can be determined by using these databases.

An important recent development is the availability of the EBI's ChEMBL database of bioactivities abstracted from the medicinal chemistry literature. Comprising 2.4 million bioactivities from more than 0.5 million compounds, much of it comprising interactions of 4,000 protein targets with small molecule ligands, this resource is set to have a significant impact on drug discovery efforts.

Resources to be covered

Catalogues of resources:

• PathGuide
• NAR database issue

Protein Interaction databases:

• Intact
• DIP
• BioGrid
• MINT
• HPRD

Data standards:

• IMEX
• PsiDev

Quaternary Structure:

• PDB BIOUNIT
• PQS
• PISA
• 3DCOMPLEX
• PIQSI
• PROTORP

Blundell group resources:

• Blundell Group home page
• PICCOLO
• CREDO
• BIPA
• TIMBAL

Prediction of Interactions

• PIPS

Hot-spots:

• ASEDB

EBI

• ChEMBL

Of these IntAct, PISA, PICCOLO and ChEMBL will be covered to the greatest depth. Numerous other resources will be touched on.

Literature References

All references mentioned in the workshop can be found here: http://www.citeulike.org/user/erice2010ppi

Suitability

This workshop is suitable for complete novices.

Course Materials

This is a "watch me" style workshop - the only requirement is an internet connection. While pre-prepared example queries will be provided attendees are of course welcome to use their "favourite" protein or PDB code instead.

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