Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers.
Each of these may include multiple 3-D conformations that are sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) root-mean-square distance (RMSD) between conformers.
In addition to the non-hydrogen atom pair-wise root-mean-square distance (henceforth termed simply RMSD), the Shape-Tanimoto (ST) value was also used as measure of the accuracy of the conformer models.
An alternative approach is an inclusion of the dispersion correction to the total energy obtained with standard DFT approximation explicitly by hand with, e.g., DFT-D method, that is atom pair-wise sum over C6R-6 potentialseese.g.e.g., Ref. [14]).
The widely used atom-pair wise dispersion correction DFT-D3 [2] is considered for comparison.
For 30 million compounds, a neighboring relationship requires a minimum of 10^14 pair-wise similarity computations.
The minimum pair-wise distances between residues for both the activated and unactivated state of each species were calculated and the smallest value was chosen for further comparisons.
The genome structure of seven N. crassa strains are divergent and not related among each other (unrooted tree analysis, minimum pair-wise dissimilarity = 0.91).
Skeletal atoms are pair-wise connected by bonds and are characterized by chemical element, integer formal charge, radical state, isotopic mass, associated implicit hydrogens, and bonds to other skeletal atoms.
A common practice is to limit the conformer count using some mix of energy-based filtering, minimum conformer root-mean-squared distance (RMSD) of pair-wise atoms, and random sampling.
