Abstract：
:A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides the Nwat parameter, the effect of the force field, the molecular dynamics simulation length, and the implicit solvent model used in the MMGBSA analysis have been also evaluated. We found that considering 30 interfacial water molecules improved the correlation between predicted and experimental binding energies by up to 30%, compared to the standard approach. Moreover, the correlation resulted in being rather sensitive to the force field and, to a minor extent, to the implicit solvent model and to the length of the MD simulation.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Maffucci I,Contini Adoi
10.1021/acs.jcim.6b00196subject
Has Abstractpub_date
2016-09-26 00:00:00pages
1692-704issue
9eissn
1549-9596issn
1549-960Xjournal_volume
56pub_type
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