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Protein Structure Computation

Protein Structure Computation. Gwyn Skone OUCL PRG Student Conference 2006. Proteins. Approximately 20–30% of body Nearly all protein ingested is retained Chain-like molecular structure Built from 20 amino acids Folds into globular state Alpha helices Beta strands/sheets

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Protein Structure Computation

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  1. Protein Structure Computation Gwyn Skone OUCL PRG Student Conference2006

  2. Proteins • Approximately 20–30% of body • Nearly all protein ingested is retained • Chain-like molecular structure • Built from 20 amino acids • Folds into globular state • Alpha helices • Beta strands/sheets • May bind to ligands • At an ‘active’ site

  3. Problems Protein Ligand • Folding • Annotation • Docking b a a - -

  4. Docking Protein Ligand • Often reversible • Geometry • Conformational change • Chemical bond potentials • Quantum effects?

  5. Drug Discovery • Bind drug ligand to protein for inhibition • Two approaches: • ‘De novo’ design • Docking • Computationally expensive • Limited precision possible on desktop • Grid computing widely employed

  6. Development • Java classes for molecule/protein model • FFT method

  7. Development • Java classes for molecule/protein model • FFT method • Pipelined architecture • New refinement procedure

  8. end.

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