Q-fit: A method for docking molecular fragments by sampling low energy conformational space

Figure 1. The docking of guanine to purine-nucleoside phosphorylase. The figure shows the RMSD (root mean squared deviation) from the crystal structure versus the interaction energy (more negative is most favourable). The top ten solutions are shown in the box with the minimized crystal structure ranked no. 5. An image of the top five generated solutions in the protein binding site shows that docking reproduces the experimental binding mode of the ligand (in red) with an RMSD of less than 1 Å in all five cases.