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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

Protein Structure Computation

Gwyn Skone

OUCL PRG Student Conference2006


Proteins
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


Problems
Problems

Protein

Ligand

  • Folding

  • Annotation

  • Docking

b

a

a

-

-


Docking
Docking

Protein

Ligand

  • Often reversible

  • Geometry

    • Conformational change

  • Chemical bond potentials

  • Quantum effects?


Drug discovery
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


Development
Development

  • Java classes for molecule/protein model

  • FFT method


Development1
Development

  • Java classes for molecule/protein model

  • FFT method

  • Pipelined architecture

  • New refinement procedure



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