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More on Charleston.......

More on Charleston. Talks given by : Adrian Elcock - Predicting functional residues Benno Schiwkowski - Visualising interaction networks Christopher Hogue -BIND A new CASP-like experiment for P-P interactions. Prediction of functionally active sites. Basic (quite clever) Idea:

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More on Charleston.......

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  1. More on Charleston....... • Talks given by : • Adrian Elcock - Predicting functional residues • Benno Schiwkowski - Visualising interaction networks • Christopher Hogue -BIND • A new CASP-like experiment for P-P interactions

  2. Prediction of functionally active sites Basic (quite clever) Idea: Claim the functionally active part of a protein is the most structurally unstable part of it (has to be "inverse" of structure it is binding to). Some evidence from mutagenesis studies. Implementation : Assume that functionally active residues will be conserved, however the same argument holds for residues which are most important for structural stability ! So, one has to try and decide which is which. Question : Can one use secondary structure prediction (or some other idea) to come up with a better implementation of this ????

  3. Visualising Networks Can one understand a network by visualising it ? No unique way of drawing a complex network, particularly in two dimensions. Very possible to construct really bad Network diagrams !!!

  4. Network of interactions for Yeast genome. • Apart from a pretty picture, almost impossible to draw any conclusions !

  5. Difficulty in interpretation if lines are overlapping - occurs in 2-dimensions • Free software available (for Windows) for intelligent drawing of networks in 2-dimensions see http://vlado.fmf.uni-lj.si/pub/networks/pajek Can avoid this if network is drawn in 3-dimensions. No free software for this ! Would need some Java applet/VRML for publications • Hard question : is a drawn network anything more than a pretty picture ?

  6. CASP for P-P Interactions • Despite the similarity of methods discussed at this conference (very much a biophysical approach, electro-static interactions, FFT's to evaluate shape complementarity, etc. ), it's still hard to compare the different methods. • Solution : equivalent to CASP experiment - entitled CompArison of PRotein Interactions (CAPRI) • Initially three examples. Groups have to try and predict final complex by mid-September. Keep doing this, with final results presented for CASP 6 • Further details can be found at http://capri.ebi.ac.uk

  7. BIND - a database of interactions • Gathers data on • Protein-Protein (P-P) interactions • Complexes • Pathways (claim to have visualisation tools, not !) • Uses ASN.1 but can be translted to XML or CORBA IDL • Networks can be passed on for mathematical analysis (e.g. Using Pajek)

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