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How many runs should I do in FITTED? PDF Print E-mail
Three runs should be enough to provide a high accuracy on any protein/receptor system. From our extensive validation that we have performed with FITTED, we have found that three runs are usually necessary in order to get the best results. However, this is highly dependent on your target. In the case of a VS, it is true that we want to minimize the computation time and avoid running the docking in duplicates or even in triplicates. Therefore, in VS benchmarks that we have performed with the latest version of FITTED, the discrimination of active against inactive molecules was not significantly affected if only one run was executed compared with three runs. However, three runs might be necessary for pose prediction in hit to lead optimization.
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