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Solvation studies of DMP323 and A76928 bound to HIV protease: Analysis of water sites using grand canonical Monte Carlo simulations
Author(s) -
Marrone Tami J.,
McCammon J. Andrew,
Resat Haluk,
Hodge C. Nicholas,
Chang ChongHwan
Publication year - 1998
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560070305
Subject(s) - monte carlo method , solvation , human immunodeficiency virus (hiv) , hiv 1 protease , statistical physics , chemistry , computational chemistry , physics , protease , biology , molecule , mathematics , virology , enzyme , biochemistry , statistics , quantum mechanics
We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV‐1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.