The focal point of this example lies within biochemistry, particularly the regulatory mechanisms of enzymes catalyzing disulfide bond formation or cleavage near the protein surface. Thioredoxins, a group of proteins, play a pivotal role in regulating, e.g., reactions of the Calvin cycle. Interestingly, a comparison of primary structures reveals the absence of a consensus motif in most thioredoxin-regulated enzymes. To uncover potential enzyme targets for thioredoxin, the examination of protein structure data is essential. The approach in this project is to find cysteine sulfur atoms within a 3 Å radius, proximal to the surface. How is this achieved? We combine the power of Jmol, AWK, and shell programming. Essential to this quest is the need for an algorithm to compute the accessible surface area of macromolecules. Fortunately, Jmol has an integrated algorithm tailored for this purpose. All files from this chapter are available from the book’s GitHub repository at CompBiol3/22_Thioredoxin .