The description of the docking results was limited. They showed results for only one docked pose for each of the four compounds. What was the basis for selecting this one pose? Often single poses are shown when it is the "best" pose as assessed by some scoring function. However, they used multiple scores, as shown in Table 1. More importantly, it is more appropriate in a docking study to show the range of poses and scores that are observed as part of defending the selection of the "best" pose. In addition, the authors should demonstrate that they have sampled a variety of docked poses and that they observe a number of clusters of poses.
[A big challenge in modeling studies is demonstrating that adequate sampling of conformational space has been done. This problem is especially acute with a target such as Abeta that has no clearly defined binding site, as noted by the authors. A proper study would involve analysis of perhaps hundreds of poses, with clustering, to demonstrate that conformational space has been adequately sampled and that the "best" poses have been distinguished from many other poses. The authors have not addressed this point.]
I think you should elaborate on reporting that particular pose for a compound. You could try to give details of how your docking algorithm works briefly, as it would mention the initial conformations generated, number of runs that were performed for each conformation and things like that. But what is good is you are using more than one scoring function, so then which the best one you decide, is the best pose reported based on one among them or it is consensus?
Thank you Alain and Mohammad for your suggestion. Mohammad I have used Molegro virtual docker.In MVD, poses found during the docking run will be automatically clustered through MVD default clustering algorithm using the RMSD threshold (1.00) criteria and only the lowest- energy representative pose from each cluster will be returned when the docking run is completed. Poses which were generated were further sorted by rerank score. By defalut it genrate 5 pose than i have selected the best one out of 5 in by rerenak score.
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