Rigid cluster decomposition of the protein MAP Kinase P38. The C-terminal domain has been artificially rigidified based on preliminary studies. The catalytically important residue PHE 169, shown in black, can be seen in the "middle" of the protein's active site. The protein contains 379 residues. The ligand was removed from the structure prior to analysis.

Movie showing 120 conformations of 200,000 conformations generated during a random FRODA run compared to a target structure. The red structures are conformations of MAP Kinase P38 (PDB Code: 1a9u). The target structure is an alternative, ligand-bound, conformation of MAP Kinase P38 that has been observer crystallographically (PDB Code: 1w82). The catalytically important PHE 169 sidechain is shown as sticks in the "middle" of the protein.

Superimposition of a MAP Kinase P38 from structure 1W82.pdb and a conformation produced by FRODA. This overlay highlights the good fit in the superposition for residue PHE 169 between the two conformations.