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Author's response: The following articles illustrate some examples of docking application to accurate prediction of protein complexes: * Prediction of multimolecular assemblies by multiple docking (PMID: 15890207).
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Open image in new window Fig. 1 An example of docking.
Table 2 Explanation of information contained in the output files of RPDOCK Column 4 RPDOCK score Column 6 8 Translation vector Column 9 11 Rotation angles Open image in new window Fig. 2 An example of docking.
AutoDock4 is acknowledged to be one of the most reliable and broadly used molecular docking tool [5], with several examples of accurate docking predictions already published [6, 7].
In addition, examples of molecular docking and molecular dynamics studies demonstrated that 34 may be the potential inhibitor to EcR and its docking conformation was similar to that of tebufenozide.
Figure 1D-G show examples of the docking configurations predicted by PatchDock, with additional examples illustrated in the Supplemental Data (Additional file 1).
Figure 3 Illustration of docking settings.
The practical example of molecular docking approach as a generic tool in SBDD of is also demonstrated.
To demonstrate how these two novel docking features can benefit the docking performance, examples of using the confined and constraint docking are shown in this section.
The above example shows the results of docking with two drugs in Curated Kinase Docking.
The DS 3.5 is also user friendly software, users can download the manual from website, please see the example for parameter setting of docking.
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