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eDIKT2 Technical Meeting

The purpose of the meeting is for edikt2 participants to share information about the technical aspects of the various activities
being funded through edikt2. The meeting is also open to other interested parties around the University and beyond.

Agenda
1330 Welcome - Jon Hill (EPCC)
1340 Jan Wildenhain (Biology) - A Chemical Genetic Matrix for Rational Discovery of Novel Small Molecule Synergies
1415 Davy Virdee (EPCC) - LSST and the University of Edinburgh
1445 COFFEE
1515 Victor Neduva (Biology) - Sequence motif atlas of protein interaction networks
1600 Salman Tahir (Biology) - Combining Chemical Cross-linking with Computer Science
1630 Discussion
1700 Close

Abstracts

A Chemical Genetic Matrix for Rational Discovery of Novel Small Molecule
Synergies
Jan Wildenhain

The density of global synthetic lethal interaction networks in yeast, estimated at some 200,000 gene-gene interaction, reflects the vast redundancy and functional interconnectivity encoded by the genome. We contend that this genetic density may be exploited to seek chemical-genetic interactions that selectively disrupt any specific mutant genotype and chemical-chemical interactions that selectively kill any target species. We have undertaken to build a comprehensive Chemical Genetic Matrix (CGM) of small molecule-gene interactions and small molecule-small molecule interactions using the budding yeast Saccharomyces cerevisiae as a model system.

The same principles of chemical-genetic specificity will apply to bacterial pathogens and to human disease states such as cancer. The CGM will cross connect genetic pathways through chemical space, identify species-specific novel antifungal agents and serve as a repository of small molecule probes across all areas of cell biology.

LSST and the University of Edinburgh
Davy Virdee

This talk will describe the challenges faced in setting up the University of Edinburgh (EPCC and the Institute of Astronomy) as a prototype Data Access Centre within the Large Synoptic Survey Telescope - an astronomy initiative in the US that
will provide digital imaging of astronomical objects across the entire sky on a nightly basis.

Sequence motif atlas of protein interaction networks
Victor Neduva

Protein interaction networks are central to most cell processes. Most of the network analysis concentrated on overall network organization with little attention to molecular basis of particular edge formation. Several computational approaches were developed to elucidate modes of protein interactions in large-scale networks. These led to discovery of novel linear motifs mediating large fraction of protein interactions. Here we will discuss details of those methods and computational issues facing large-scale pattern discovery in the noisy biological data.

Combining Chemical Cross-linking with Computer Science
Salman Tahir

Chemical cross-Linking of peptides coupled with mass spectrometry is a powerful method to investigate protein structure and protein-protein interactions. When applied to single proteins or small purified protein complexes, this methodology works well. However certain challenges arise when applied to more complex samples. One of the main problems is the combinatorial increase in the search space that occurs when all peptide-peptide combinations are considered in a database search.

We have developed an algorithm that finds and validates cross-linked peptides in an efficient and scalable manner by adopting a number of principles both biologically and computationally. Firstly, we make use of a high accuracy library of over 1000 synthetic peptides to understand the fragmentation behaviour of cross-linked peptides. Using this information we are able to reduce the complexity of searching to essentially two successive searches of linear peptides as opposed to analysing every possible combination ofpeptides that could potentially cross-link. We achieve further speedup using parallelization and data-structures that complement the nature of the data we search. Our novel computational approach enables us to address large protein complexes and, as a result, facilitates the construction of low-resolution 3D models of cellular machineries that cannot be studied by
current structural analysis tools.

For further details and registration, please contact:
- Jon Hill j.hill@epcc.ed.ac.uk

Location: 
Rm 720, Swann Building, Kings Buildings
Dates: 
5 Dec 2008