This film illustrates some of the forces which interact to create the poing protein model. The first 30 seconds shows a cartoon of PDB 1res, and displays the state of the protein at every interation of the simulation. The next 30 seconds shows the points the model simulates, and the most basic forces which keep the modelled protein together, shown as rods between the points. Black rods are repulsive forces, and white rods are attractive forces. The final 30 seconds shows all of the forces in the model together.
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This film shows two proteins being simulated, with increasingly coarse sampling of the iterations in the model, creating a "timelapse" effect. Initially PDB 1res is used as a simple example, then the film switches to PDB 1ten to illustrate large-scale rearrangements of secondary structure units.
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This film shows spinning images of a cross-section of the structures produced by our model, aligned with the known native structures. In each case, the native is shown in pale colours, and the poing structure is shown in brighter colours. The label below each is the PDB code for the model, the TM score of the structural alignment between our structure and the native, and a short description of the protein. The first alignment shown is the worst, and then they are shown in order of increasing quality.
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Films and text © Benjamin Jefferys 2007