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Parameters used in the docking process are shown in Table 2.
Eventually, the top 10000 (pharmacophore) molecules were chosen to the docking process.
Considerable reduction in binding energies was recorded along the docking process.
This significantly reduces the cost of clique detection and consequently increases the efficiency of the docking process.
One possibility to overcome these problems is the inclusion of additional, preferably experimental information in the docking process.
The issue considered in this paper is the dynamic behavior of flexible probe based on space probe-cone docking mechanism in the docking process.
Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally.
The elastic energy originates from the attractive force between myosin and actin, and accumulates during the docking process.
This offers the big advantage to setup the docking with a great graphical interface, as well the created pharmacophores can be used to guide the docking process.
For achieving this, we aim at studying the impact of the two preparation schemes on the chemotype recognition during the docking process in a subsequent publication.
Two features have been incorporated in the program suite that allow for user-defined guidance of the docking process based on previous experimental data.
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