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Last Modified 7 Sep 2007 |
Docking Study
A compound is superposed on the ligand-binding site of a target protein in terms of the structure-based manner. The superposition is carried out using flags or grids representing a certain chemical property of the compound and the ligand-binding site (this chemical property brings about individual properties of docking programs). In general, the ligand-binding site of a target protein is treated as a static state. In this case, an induced fit effect and any effects of protein side chains are approximated by the force field potentials. Recently, a flexible docking which simultaneously considers an induced fit effect of the side chain in a ligand-binding site is becoming mainstream in the docking study. Note that most of the docking programs are termed as the FLEXIBLE docking program, although they treat only the compound flexibility. Once superposition succeeds, each torsional bond of the superposed compound in an initial structure is rotated at a certain rotation angle (30°, 45°, 60°, 90°, or 120°). Subsequently, the interaction energy for all docking modes accompanying to the rotations of the torsional bonds is calculated using the structural optimizations. In this docking algorithm, the number of simulations is reduced in but the accuracy of dockings is lowered. To avoid this problem, the docking program carrying this algorithm needs to prepare some initial structures per single compound.
After being optimized, the individual docking modes are assessed by an energy function which is carried in the individual docking programs and has been tuned for the current target protein. In general, most of the docking program adopting the grid algorithm calculate a score value rather than the interaction energy, since the grid algorithm largely simplifies the energy calculations. A compound that adopts higher score in these modes is suggested as a candidate for the target protein molecule.
See our protein- and ligand-flexible multiple-compound docking simulation program, Docking Study with HyperChem, which carries out a novel and most powerful docking algorithm. Moreover, this program can also perform true flexible docking which can consider the side chain and main chain flexibilities of the whole protein molecule as well as the compound flexibility.
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