If you've played FoldIt for awhile, you have undoubtedly asked yourself "is it better to concentrate my efforts on hand-folding, or on scripts?"

The answer: "Yes!"

Both are equally important; and their combined effect is synergistic.

Setting up the analogy

To illustrate, consider the following analogy of washing dishes. A dish is equivalent to one segment of a protein. One might choose to wash dishes by hand, which corresponds to hand-folding, or one might use an automatic dishwasher, which corresponds to using scripts.

Before automatic dishwashers were invented, folks had to manually grab each dish, run the sponge over it, top and bottom, maybe even use the scraper on the tougher stuff. Then rinse the dish, and place it in the rack to dry, or dry it by hand. With a large number of dishes, this could take hours.

Then the miraculous automatic dishwasher was created, probably by someone frustrated with the lengthy manual approach. Load those dishes, add soap, turn it on, and --- VOILA! --- clean dishes, within minutes. Some of the time. Often, dishes still had food waste stuck on them when the cleaning cycle finished.

The problem was, the person loading the dishwasher placed the dishes willy-nilly in the machine, with no rhyme or reason to the arrangement. Cleaning results were erratic, and often worse than if the dishes were washed by hand.

Scripting is like using a dishwasher? Really?

Jumping to folding....

Manually washing dishes is laborious and time consuming. Given enough time and effort, however, it usually produces good results. Manually working a protein is laborious, and time consuming. Given enough time and effort, it usually produces good results.


a sample listing from a player's script library

Using a dishwasher automates the process of washing dishes, is easier, quicker, and when done right, produces good results.

Using a script automates the process of folding, is easier, quicker, and when done right, produces good results.

Running a dishwasher without first scraping off the dishes and then loading them correctly (both highly manual processes) produces inconsistent results.

Folding solely by scripts without first manually working the protein into a better structure produces inconsistent results.

Washing dishes by first manually scraping off the worst food residue, then properly stacking them in the dishwasher, and then running the automatic dishwashing routine on the machine nearly always produces excellent results.

Folding a protein by first manually working on worst red parts, then properly placing the secondary structures in appropriate places, and then running scripts on the machine nearly always produces excellent results.

The best results are made by an appropriate marriage of manual and automatic methods.


Manual folding is essential. Scripting is essential. Doing both is most essential to getting the best results.

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