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RAPPER

RAPPER. Nick Furnham Blundell Group – Department of Biochemistry Cambridge University UK http://raven.bioc.cam.ac.uk. RAMPAGE. Tool for generating Ramachandran plots for structure validation. Stripped out of RAPPER.

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RAPPER

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  1. RAPPER Nick Furnham Blundell Group – Department of Biochemistry Cambridge University UK http://raven.bioc.cam.ac.uk

  2. RAMPAGE • Tool for generating Ramachandran plots for structure validation. • Stripped out of RAPPER. • Defined file structure (will use as basis for RAPPER) in CCP4 main distribution. • Have autoconf build working (thanks Charles). • Have windows build (thanks Francois). • Have replaced the Ramachandran plot from Procheck in validation CCP4i window (thanks Peter and Martyn)

  3. RAMPAGE

  4. Sampling • Major degrees of freedom are from the φ / ψ / ω. As sampling is a cpu intensive procedure only consider φ / ψ fix ω to 0 or 180 • Use fine-grained residue specific φ/ψ state sets. • Also sample side chain rotamers from a detained hand-curated side chain conformation libraries

  5. Constraint & Restraint • When searching optimising on: • Implicit Constraints: • Ideal Engh & Huber stereochemistry • Van der Waals overlaps: • Efficiently checked for by a grid based cache • Arbitrary Restraints: • Positional restraints • Experimental Data e.g. X-ray electron density • Framework restraints • Secondary Structure

  6. Sampling

  7. RAPPER • By going through the process with RAMPAGE now have bases for integrating RAPPER. • Latest development has been to bug fixed and extended to cope with SeMet (modelling and accounting for heavy atom scattering) and other heavy atom scatters in internal map calculations. • Now have a frozen working development. • Have a 32bit Linux distribtion but problems in transporting to 64bit (int casting issues) • Can force through compiler but is this cross platform solution – any ideas?

  8. RAPPER • How to integrate into suite – what functionality is best to concentrate on? • We would like to start with loop generation given weak density. • Can also have multi-model ensemble generation using automated rebuilding and refinement or rebuilding entire structure or low resolution hypothesis testing

  9. RAPPER • Research directions: • Multi model conformations for multimeric structures to study heterogeneity and uncertainty in protein-protein interfaces. • Resolving CASP targets from CASP7 • In discussion with Garib about using RAPPER to provide a ‘bootstrap’ map. • Now have developed RAPPERtk - an extrapolation of RAPPER to allow extension to modelling strategies. • Now includes RNA / DNA conformer modelling • EM envelope fitting • Ligand modelling • Nearly can cope with NMR data!

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