Lost focus for gamers

Started by Cyberkashi

Cyberkashi Lv 1

When I first started folding a few years ago the puzzles and tutorials made sense to gamers who wanted to contribute to science but didn't really have any science background.

Over the past several months, the puzzle information has gotten way more science technical with no explanation for those of us without the science / biology background. The tutorials are still focused on manipulating the protein without much science context.

For example, I am working on 1129: Unsolved De-Novo Freestyle.
The structure of this protein is still unknown. The PSIPRED secondary structure predictions are
provided on the starting model.

 Sequence:  MTVSRSTGDHRRTSKLFLLFRMEGDRYALDAREVVEVLPLLRLKRIPEAPEWVAGVFSHRGVLVPVLDLCAMAFGRAALART   
            STRIVLVEYRARQDREPVWLGLILEQATDTLRCEPSAFRDYGLDNGGARYLGPVYEGPRGLVQWVRVEALLPDEVRALLFPPECGEGAA

You lost me after the "the structure of this protein is still unknown." I understand that the amino acids in the protein go in an order. But I don't understand what this order means to me in relation to the folding puzzle. I would be helpful to have more extensive, yet simply written explanations of what we were trying to accomplish in the puzzle for those who don't have a background in proteins and biology.

jeff101 Lv 1

Some good links to learn the basics:

http://fold.it/portal/info/about

http://foldit.wikia.com/wiki/Foldit_Wiki
look in the left column under "New Players"
or in the right column under "The Science".

The sequence given above can fold many different ways.
Some of these folded structures are more favorable than others.
The more favorable ones should give higher Foldit scores.

Each letter in the sequence stands for an amino acid.
Some amino acids are nonpolar or hydrophobic.
They get colored orange if you color by hydro
and generally end up in the protein interior.
Other amino acids are polar or hydrophilic.
They get colored blue if you color by hydro
and generally end up in the protein exterior.

Each amino acid has different roles (see for example
http://foldit.wikia.com/wiki/Amino_Acids). Some tend to occur
in helices, some tend to occur in loops, and others tend to occur
in sheets. Some like C for cysteine can bind to each other to form
disulfide bonds (see for example https://fold.it/portal/recipe/43861).
Others like G for glycine are very small and flexible. P for proline
tend to put kinks in the protein backbone. Some amino acids have small
sidechains, others have large sidechains. Some have no charge, some
have positive charge, and some have negative charge. Positive ones can
attract negative ones to form salt bridges. Positive ones can repel
other positive ones. Negative ones can repel other negative ones. Some
amino acids have sidechains that can participate in hydrogen bonds
(see for example https://fold.it/portal/node/2000666).

bkoep Staff Lv 1

Thanks for the feedback, Cyberkashi!

It's always a balancing act for us: On one hand, we'd like to provide simple explanations and broad ideas for newcomers; on the other hand, we want to make sure all the complex details and nuanced data are available for the hardcore veterans.

It's helpful to hear that we may have skewed the balance—in the future we can try to be a little more explicit for those without the technical background!

Cyberkashi Lv 1

My thanks to each of who shared suggestions, explanations and links. They are very helpful and much appreciated.

– Cyberkashi