Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

Accurate prediction of protonation state

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

✍ Kitiyaporn Wittayanarakul; Supot Hannongbua; Michael Feig 📂 Article 📅 2008 🏛 John Wiley and Sons 🌐 English ⚖ 531 KB

## 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 enzym