We used maximum likelihood estimation, which is the most commonly used supervised classification method in the field, as implemented in the ENVI software.
To calculate the total energy of the PFP crystal, we use empirical interatomic force fields, in particular, the MM3 force field as implemented in the TINKER code, and further checked the influence of the particular choice of force field on the structure solution.
To generate the starting structures, we first performed molecular dynamics simulations at 298 K with the molecular mechanics MMFF94 force field as implemented in the software Tinker.
This influence is quantified by the scoring and rmsd values before and after minimization, and we compared these results to those produced by a minimization under the MAB force field as implemented in the program Moloc [4].
To this end, we also utilized the DREIDING force field as implemented in the GULP code, which led to the same structure solutions as already found with MM3.
Molecular dynamics (MD) simulations were conducted using the OPLS-AA force field as implemented in the Q simulation package (version 5.06).
The force field used for the receptor modeling in this study was Amber99 62 with R-field solvation, as implemented in the MOE software.
This paper describes our current work in these fields as implemented in the in-house program FEM90.
The robustness of the structure was monitored through analysis of plots of the Anolea mean force potential [99] and GROMOS [100] empirical force field energy, as implemented in the workspace.
Three separate coevolution calculations on the alignments were carried out using PSICOV v2.1, mean field DCA as implemented in the FreeContact package (Kaján et al., 2014) and CCMpred (Seemayer et al., 2014).
