Additional file 1: of Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance
Dynamic changes of pocket volumes of three wild type protease-PI complexes during 10 ns molecular dynamics simulation. The three wild type protease-PI complexes (DRV_0, LPV_0, and NFV_0) contain single residue substitutions S37N, L63P, and V3I respectively that contributed to shrink the PI-binding pocket as compared to the native protease [PDB:1ODW]. The fluctuation of pocket volume of the native protease is estimated based on the three PIs (DRV, LPV, and NFV), and is shown in gray shade (~1955 ± 213 Å3). The molecular dynamics simulations were performed in standard protocol for 2x5ns using AMBER14. (PDF 564 kb
