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Cover Feature: AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein–Ligand Association (ChemMedChem 6/2018)
Author(s) -
Cuzzolin Alberto,
Deganutti Giuseppe,
Salmaso Veronica,
Sturlese Mattia,
Moro Stefano
Publication year - 2018
Publication title -
chemmedchem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.817
H-Index - 100
eISSN - 1860-7187
pISSN - 1860-7179
DOI - 10.1002/cmdc.201800125
Subject(s) - feature (linguistics) , molecular dynamics , cover (algebra) , molecule , ligand (biochemistry) , chemistry , cutoff , function (biology) , statistical physics , physics , biological system , computer science , computational chemistry , engineering , biology , mechanical engineering , philosophy , linguistics , receptor , biochemistry , organic chemistry , quantum mechanics , evolutionary biology
The Cover Feature shows the different behavior of structural water molecules and bulk water. We have developed the AquaMMapS tool, which is able to identify stationary hydration sites close to the protein surface starting from molecular dynamics simulation. Root‐mean‐square fluctuation (i.e., a 1.4 Å cutoff) is employed to discriminate stationary from nonstationary water molecules. Space is organized into a grid, where cells crossed by stationary water molecules are selected and their occupancy computed along the simulation. Moreover, an empirical scoring function, the AquaMMapScore, has been developed to evaluate the penalty of a ligand displacing a stationary water hot spot. More information can be found in the Full Paper by Stefano Moro et al. on page 522 in Issue 6, 2018 (DOI: 10.1002/cmdc.201700564).