My suggestion is to add an easy way to get the sequence of the protein. I think it's important becuase that provides very useful information, like the possible secondary structure information of the protein (and make things easier in the "quest to the native" puzzles), check if there are transmembrane segments, among others.
Any comments or suggestions about this idea are welcome.
Best Regards
Marco Ambriz
Well, you can read and write the secondary structure by script, but you can't store it.
So, my addition to your suggestion is a save function!
Pardon, what are transmembrane segments?
every living cell (and some viruses) has a membrane that envelopes them (compare it to our skin that forms the barrier between our organism and the rest of the world). Now these membranes are full of proteins on them or even in them. These proteins are attached to the membrane by stretches of amino acids that are located in the membrane and can form a sort of anker for that protein. The stretch of amino acids that is located there would then be a trans-membrane segment as it goes through the membrane. Since the membranes are formed by lipids (hydrophobic), the amino acids found in these segments are also mainly hydrophobic, so you can start with statistics and recognition of patterns in the sequence that would be more/less probable of being located in the membrane (and also the structure) etc.. That's in short..
Now as for me to contribute to the discussion.. I would say that looking up all info you get from the sequence is a job that is already done at the moment you get the puzzle. If you would be looking up the secondary structure predictions etc, you would actually be doing the same as computers, and foldit just tries to see what people can intuitively do, no? So I don't really see the point yet in having the sequence for that purpose.
I would like to see the sequence of the protein though. For instance on top of the screen and when you are on an amino acid, you would see the corresponding letter in the sequence highlighted. Or see which amino acid you have when you click on it. This could be useful as every amino acid has its own properties, some of which are very important to structure. For instance you would know that Pro or Gly can be bad in helices etc. If you know the amino acid structures, then that's ok, but it could help learning the amino acids and their properties for those who do not recognize it or just know nothing of biochemistry.
you can now save aa sequence from the local scriptlog file
How can I see the amino acid labels and what I have actually done in the game. I am a beginner and would like to use Foldit to lean the properties of amino acids and the way they act? I read something about saving the scrip but I don’t fully understand how to do that in the Windows application.