Dataset showing the impact of the protonation states on molecular dynamics of HIV protease

The data described here supports the research article “Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations” (Soares et al., 2016) [1]. The data involves both standard Molecular Dynamics (MD) and Constant pH Molecular Dynamics (CpHMD) to elucidate the effect of protonation states of catalytic dyad on the HIV-PR conformation. The data obtained from MD simulation demonstrate that the protonation state of the two aspartic acids (Asp25/Asp25′) has a strong influence on the dynamics of the HIV-PR. Regarding the CpHMD simulation, we performed pk(a) calculations for HIV-PR and the data indicate that only one catalytic aspartate should be protonated.