There are several ways to calculate the PMF in |Gromacs|, probably the most common of which is to make use of the pull code. The steps for obtaining a PMF using umbrella sampling, which allows for sampling of statistically-improbable states, are: * Generate a series of configurations along...
We carried out a meta-analysis of the experimental literature reporting time-courses of protein refolding and acquisition of function (Fig.1aand Supplementary Data1). We focus on in vitro studies because they are capable of controlling for a number of factors that are currently not possible to c...
Additionally, the Lorentz force equation can be used to calculate the deflection of a plasma jet by a magnetic field, taking into consideration factors such as electric fields and self-induced magnetic fields. The kinetic energy density of the plasma must overcome the magnetic energy density of ...
We carried out a meta-analysis of the experimental literature reporting time-courses of protein refolding and acquisition of function (Fig.1aand Supplementary Data1). We focus on in vitro studies because they are capable of controlling for a number of factors that are currently not possible to c...
We next asked how it is possible that long-lived misfolded proteins are able to bypass the post-translational cellular chaperone machinery. To address this question we used coarse-grained Langevin dynamics to calculate the dissociation constant between the chaperone GroEL and three distinct conformational...
(G, N, P, Q, S, T) and hydrophobic (A, C, I, L, M, V) amino acid residues (hydrophobic and polar, respectively), and fractions of residues of A, L, and S. Notably, except for the pLDDT of AF2 models, the experimental ProS structures were employed to calculate the structural ...