(A) Schematic of the thioredoxin active site of training structure 2FWH. The environment around each active site cysteine sulfur atom is segmented into six concentric radial shells, each 1.25 Å thick.
(B) Thioredoxin active site of dynamic FEATURE true positive 2DJJ. Shown are the starting PDB conformation (left) and the highest scoring conformation from molecular dynamics (right).
(C) Thioredoxin active sites of dynamic FEATURE false negatives 1WMJ and 2ALB. In (A), (B), and (C), residues near the active site are shown using a ball-and-stick schematic and atoms within 7.5 Å of the active sulfur atoms are colored (C = green, N = blue, O = red, and S = yellow). The conserved cysteines and proline are highlighted by colored covalent bonds. FEATURE scores for the active cysteines are below the panels.
(D) RMSD distribution of conserved active site residues. Standard box plots show RMSD between the static training proteins and the simulation ensembles of the training proteins, 2DJJ, 1WMJ, and 2ALB. Simulation frames are split into high and low FEATURE scores for active sites scoring above or below model thresholds, respectively.
(E) Multi-site thioredoxin FEATURE model fingerprint. The fingerprint shows the physicochemical properties significantly over-represented (abundant, red) and under-represented (deficient, blue) in the local environment of the active cysteines. Color intensity reflects a property’s significance (p-value) with a minimal inclusion threshold of 0.01.