Editing Foldit Jargon 101

As if biochemistry weren't enough, foldit's designers and players have added their own jargon to speed up communication and confuse new players. Here are some of my favorites in the jargon category.

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==segment, residue, AA, backbone, sidechain, structure...==
This part contains mostly real biochemistry terms, stand back.

Foldit is about folding proteins. A protein is a '''chain''' of '''amino acids '''(or '''AA'''s). There happen to be 20 amino acids at play in foldit. In a protein, each amino acid in the chain is called a '''segment''' or a '''residue'''. Each segment or residue has a number, from one to the number of residues in the chain. The chain is actually built in the numeric order. Some protein viewing tools (but not foldit) show arrows at the end of structures in the protein. The arrows point toward the end (highest-numbered residue) of the protein.

The chain of amino acids is the '''backbone''' of the protein. Each amino acid can have a part that sticks out from the backbone, called the '''sidechain'''. The shape of the sidechain makes it possible to identify each amino acid on sight in foldit, if View Sidechains -> All is selected and you studied biochem or played foldit a long, long time.

The order of the amino acids in the protein is the '''primary structure''' of the protein. Certain sequences of amino acids tend to form flat '''sheets''' or coiled '''helixes'''. Parts of the protein that aren't in a sheet or helix are called '''loops'''. The sheets, helixes, and loops make up the '''secondary structure''' of the protein.

Some foldit puzzles start with the protein as a straight '''extended chain'''. An extended chain may have sheets and helixes identified, or it may be one long loop. Other foldit puzzles start with the protein already partly folded. The overall way that the protein is arranged is called the '''tertiary structure''' of the protein. The way that a protein is arranged at a given point in time is called a '''pose'''.
==shake and wiggle==
Shake and wiggle are the most basic foldit tools. They both move the protein around a little in hopes of improving the score.

The "shake" tool affects only the sidechains. The shake tool automatically shows all the sidechains, and you can actually see them moving around as the shake runs.

The "wiggle" tool moves the backbone as well as the sidechains. We don't know the exact details of how it works, but a "wiggle" is more gentle than a "shake". There are actually three types of wiggle -- "wiggle all", which does backbone and sidechains at the same time, and also "wiggle sidechains" and "wiggle backbone" for separate action. (On Windows, hotkeys "w", "e", and "t", respectively.)
==stabilize, qstab, fuze==
"Stabilize" means shaking and wiggling the protein a little bit after a change. The goal is get the protein to a relatively stable point without spending too much time. A "quick stabilize" limits the amount of shaking done, usually to one cycle. In most cases, additional shaking produces little additional score.

"Fuze" involves changing the clashing importance (CI) in addition to shaking and wiggling. A fuze typically sets a low CI (for example, 0.05) then shakes and wiggles, followed by a wiggle at CI 1.0. Most fuzes repeat this process several times, increasing the low CI each time. The results of a fuze will normally be more stable and higher scoring than the results of a stabilize alone.

Both stabilizing and fuzing can be done manually or scripted. Most advanced scripts attempt to stabilize the protein first. If the results look promising, scripts then try fuzing.

==DRW and EDRW and TvdL==

"DRW" stands for "Deep Rebuild Worst", which is a type of recipe or script. A DRW script finds the parts of the protein that are the scoring the worst, and then rebuilds them. The best rebuild gets further attention to see it improves the score.

The original DRW was created by rav3n_pl and others. EDRW means "enhanced DRW", specifically DRW as enhanced by Timo van der Laan. Timo is also known as TvdL.

The latest EDRW recipe from TvdL is "TvdL Enhanced DRW 2.3.1", released December, 2013.

==GAB==

"GAB" stands for "Genetic Algorithm Banding", and is proof that many people have trouble spelling "algorithm".

Unlike DRW and other rebuilding scripts, GAB makes random changes to the protein using rubber bands in attempt to improve the score.

GAB starts by creating groups of bands called "critters". Each band in a critter has a random length and strength. GAB tests the results of each critter. The best-scoring critters are kept for a new generation. New critters are added to each generation to replace critters that's didn't make the cut. Some new critters are random, and some are the results of "breeding" critters from the previous generation.

Like DRW, rav3n_pl is the author of the prototypical GAB recipe. "Rav3n_pl GAB v2.0.6", last updated February, 2013, is widely used. There is no "EGAB", but there are many variations.
==ZLB and BiS==
ZLB stands for "zero-length band", and refers to a rubber band that isn't attached to the protein on one end. If you right-click on such a band and check its length, you'll see it's zero. [[File:Zlb.png|frame|Zero-length band]]

A zero-length band still pulls on the protein. A zero-length band just pulls the attached end of the band toward the unattached end. A regular attached band pulls the two sections of the protein toward each other.

ZLBs still have a length...it's really that the "target length" property is not defined for a band with an unattached end.

A short ZLB can be used to help keep part of the protein where it is. Various scripts like "Zero Length Bands v 2.0.1 -- Brow42" use this behavior.

"BiS" stands for "bands in space", which is another way of saying zero-length band, but maybe a longer zero-length band. Many banding recipes attach one part of the protein to another, but recipes like "Rav3n_pl GAB BiS v2.0.1" create bands with unattached ends.
==more fun band with bands==
Non-zero length bands, which connect one segment of the protein with another, start with a default length of 3.5. (The unit of length seem to be '''angstroms'''.) If the two ends of the band are farther apart, the band will pull them together. If they are closer, the band will push them apart. You can change the length of the band to determine whether the band pushes or pull.
==mojo and stickiness; guides and clouds==
The term "mojo" was used early on by foldit players to describe the tendency of a protein to return back to its current shape after a change. For example, if you move one end of the protein and start to wiggle, you may see other parts of the protein change. Your carefully aligned sheets may start to come apart. If they start to go back into alignment, your protein has "good mojo". In general, mojo is a good thing.

The amount of mojo is determined by the overall shape of the protein and bonds between different parts of the protein. In foldit, there are a couple of sources of "stickiness" that may help shape the protein.

Certain foldit puzzles provide a "guide", which is a shadow version of the protein. (A saved solution can also be loaded as a guide.) The guide itself seems to be slightly sticky, although it's hard to be sure. Puzzles with a guide are sometimes called QTTN for Quest To The Native, with the goal of getting to protein folded to match a known solution.

In electron density puzzles, the electron density cloud is another type of guide. As with a regular guide, you drag or band to align the protein with the cloud. Once in the cloud, there again seems to be a tendency for the protein to stick.
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