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- W1966720984 abstract "Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities." @default.
- W1966720984 created "2016-06-24" @default.
- W1966720984 creator A5020458772 @default.
- W1966720984 creator A5043774189 @default.
- W1966720984 creator A5061800523 @default.
- W1966720984 date "2008-01-01" @default.
- W1966720984 modified "2023-09-27" @default.
- W1966720984 title "Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors" @default.
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- W1966720984 doi "https://doi.org/10.1002/jcc.20821" @default.
- W1966720984 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17849388" @default.
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