My knowledge of Chinese symbols is very limited. Apparently sometimes symbols suggest that which they represent. Here's an interesting site with information about both pictographs and ideographs. Sometimes the relationship between symbols and meaning can entail arbitrary assignment of symbols to meanings. I believe I have an inkling as to what the software designers had in mind when they chose Chinese characters to model protein folding dynamics but since I do not have it from the source I'll instead focus on protein properties.

A major focus of the linked paper seems to be evolutionary transitional states where new functions are enabled by changes in the amino acids of proteins. Modularity is featured in that within major protein families certain commonalities are shared by family members. For example, alpha helices, are structural elements found in proteins. They can be particular to a protein group. A basic structural feature may be common to proteins found in group x while a different feature may mark proteins of group y. Differences between proteins in group x may involve small variations in protein structure. Slight refinements of a basic shared template.

Interestingly enough sometimes a single amino acid substitution, if at a critical juncture, can have a large impact on the folding of that protein thereby affecting protein shape. Structure is critical to protein function. Changes in protein structure impact function giving rise to significant phenotypic effects from small changes in genotype. The idea of newer software is more accurate predictions of how changes in the primary structure of proteins impacts the tertiary structure of those same proteins.

Bilbo: Now can't one add onto Chinese characters by adding a mark or something, and expand their meaning? Say, for example, from "ball" to "green ball"?

No, not really. At least not in any sort of arbitraty way. Many of their characters are sort of composites of other characters though, like you might find 小 (small) and 亻(an alternate form of 人, or "people") as part of another larger character, say 你 (you). So the three radicals that form "you" can sort of be thought of as meaning "small equal people." That doesn't mean you can just toss a 小 into another character to make it a "small whatever."