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Protein Structure Computation: Insights and Challenges for Drug Discovery

Discover the world of protein structure computation at the PRG Student Conference 2006. Delve into the molecular intricacies, folding patterns, and binding interactions of proteins. Learn about the methods and challenges in drug discovery through protein-ligand interactions. Explore the development of Java classes, FFT methods, and refined procedures for enhancing computational precision in studying proteins.

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Protein Structure Computation: Insights and Challenges for Drug Discovery

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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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