1 / 8

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:

cyndi
Download Presentation

More on Charleston.......

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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)

More Related