Protein Structure Computation Gwyn Skone OUCL PRG Student Conference 2006

1 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

2 Problems  Folding  Annotation  Docking      Ligand Protein

3 Docking  Often reversible  Geometry  Conformational change  Chemical bond potentials  Quantum effects? Ligand Protein

4 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

5 Development  Java classes for molecule/protein model  FFT method

6 Development  Java classes for molecule/protein model  FFT method  Pipelined architecture  New refinement procedure

end.