The Nwat-MMGBSA {method|technique|approach|strategy|system|process}, whose theory has been described in Maffucci & Contini, JCTC 2013, 9, 2706, is based on the inclusion as part {of the|from the|in the|on the|with the|of your} receptor of a given number of water molecules (Nwat) which are the closest to a residue (generally the ligand) or to a selection of residues (the contact interface) in each frame {of the|from the|in the|on the|with the|of your} MD simulation. The {method|technique|approach|strategy|system|process} was shown to improve the correlation between predicted and experimental binding energy in both ligand-receptor and protein-protein complexes (Maffucci & Contini, JCIM 2016, 56, 1692). Here, we report on the optimization {of the|from the|in the|on the|with the|of your} Nwat-MMGBSA protocol for its use to rescore docking {results|outcomes|final results|benefits}. We also report an automatic workflow, based on three independent scripts (which can be concatenated in a fully automated procedure) to easily employ Nwat-MMGBSA rescoring in virtual screening application. The protocol has been tuned using three different examples, and then tested in two retrospective virtual screening examples. In each example, the Nwat-MMGBSA {method|technique|approach|strategy|system|process} has been compared with the standard MMGBSA approach (Nwat=0). A link to download the scripts, working examples and tutorials is also provided. Price of 1622843-37-1 Buy1003309-09-8 PMID:24118276
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