When starting de novo, I try to make the hydrophobicity on the same size for successive sheets.
However, the starting flat protein often reverse the hydrophobicity between successive sheets.
Is there a reason for this default alignment?
S0c, Maybe this will give you some impetus to keep going ?
https://alz.org/
http://www.alsa.org/
Amino acids are combined into proteins by ribosomes.
The ribosome chains each amino acid to the next by a peptide bond. The first amino acid in the chain (now called a "residue") becomes segment 1 in Foldit. It's the first to leave the ribosome, but the rest of the chain soon follows.
Fun fact, methionine is always the first residue, see start codon. The starting methionine is often removed in post-translational modification.
For the second part, take a look at "protein palidrome" or "peptide palindrome". Partial protein palindromes are popular, and even pervasive in the PDB.
Check out A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins from 2008, which states:
One might expect that reversing the sequence would result in folds that are mirror-images of the original fold. However, there exists theoretical and experimental evidences that sequence reversing results in the same rather than the mirror folding, presumably due to the fact that both native and reverse proteins have the same amino acid compositions and/or similar hydrophobic-hydrophilic patterns. Evidence suggesting reverse peptide sequences result in different structures has also been presented in the literature.
So perhaps a perfect protein palindrome is possible…or perhaps not.
Supporting a great cause is, indeed, well, great. I won't argue with that!
But my focus is more on the game aspect. How can Foldit as a game stand on its own two feet and keep people playing in absence of the citizen science aspect? I do acknowledge that a game is the sum of its parts and nothing is ever in isolation, but I find it to be one of the weakest aspects of Foldit right now, and a major roadblock for me to promote playing it to my friends.
Edit: As I was publishing this a relevant quote came to mind that sums up my stance. Here's a 6 second clip of the current President and COO of Nintendo of America, Reggie Fils-Aime: https://www.youtube.com/watch?v=3MlNWYyVdh0
The 1 minute monologue that this clip is from was from E3 2017, talking about the Nintendo Switch.
Is it possible to simulate a hydrophobic region in Foldit for the sake of puzzles involving proteins with external hydrophobic domains for cell membranes? I've always wondered about designing little cellular molecular spaceports for receptor molecules and having a little fun with that.
Is it possible to have some of the Monomer Design Puzzles be for membrane proteins, with hydrophobics on the protein exterior and hydrophilics in the protein core? That would put a new twist on a common puzzle type. Would the Building Blocks in the Blueprint tool be the same for membrane proteins? Would remix & rebuild need to be changed to treat membrane proteins?
My Foldit experience has raised my interest in becoming formally educated in bioinformatics. Is there a way for non-US citizens to attend online courses with certification in this field by either University of Washington or UCDavis ?
I may not be able to attend the online chat, but an answer to the question would be much appreciated for later offline reading.
There are a lot of options for continuing education, and the best choice will depend on your specific motivation/intention. UW does offer a handful of online programs that accept international applications, and you can read about them here:
https://www.pce.uw.edu/online
It's worth noting that many online programs do not offer accredited degrees, but only award a "certificate" upon program completion. These certificates are no substitute for a university degree, which is a strict requirement of many job applications. My understanding is that these certificates are most often used to boost the résumés of university graduates who are otherwise qualified, but are simply looking for a leg up when applying for jobs in very specific fields (e.g. a graduate with a bachelor's degree in biology might pursue extra certification before applying for competitive jobs in the pharmaceutical industry).
If you have in mind something in particular, feel free to send me a PM and maybe I can offer more pointed advice!
The answer in the chat is what I wanted: this starting rotation has no meaning and I may rotate successive sheets like I want.
Thank you