Hand folding tutorial process

Case number:699969-2000267
Opened by:Skippysk8s
Opened on:Tuesday, January 27, 2015 - 02:23
Last modified:Tuesday, January 27, 2015 - 19:43

Many of us have never seen a hand fold puzzle until the last couple weeks. The big proteins are overwhelming me and likely others -- even to some who do quite well with other types of puzzles.
Can we develop a tutorial track that progresses from simpler to more complex hand folding puzzles? No need for points, just a way to practice and get feedback. Once I get past putting a sheet plane together, my puzzles fall apart. I get the theory, but I need practice
Alternatively, I may just go back and look for expired puzzles to work with smaller proteins. But hints along the way would be useful, such as how to get a helix to stay on the hydrophobic side of a sheet, or when a sheet plane really should be split. I want to improve skills --just need something a little smaller and more manageable with hints along the way

(Tue, 01/27/2015 - 02:23  |  3 comments)

Joined: 09/24/2012
Groups: Go Science


I had the same problem until I looked to the following videos:

It takes some time but you learn a lot from the best de novo and hand folding players. It's good to watch from session 1 to 6 (the latest one from susume is quite more scientific, but I found it particularly inspiring for design puzzles).

Good luck !

Joined: 09/24/2012
Groups: Go Science

Concerning the sheet problem: once you have a nice structure, protect it with bands (between the sheets), with freezes (freeze the sheet and the loops between the sheets). IdealSS the helixes, and freeze the helixes too.

Then use only local shake & wiggle on the red segments (view = relative scoring). This can been done unfreezed too.

Also shake all, wiggle sidechains all (mutate all on design puzzles).

Never use wiggle backbones of wiggle all on unprotected structure if score <7000.

Only when you have almost positive points, you can try a wiggle backbones but with all good structures freezed and/or banded.

Any time you looze your structure, "undo" and try anything else. To keep the structure is the most important untill you get almost 7000 points.

Save your work, then try using GUI scripts. This starts with "multiple local wiggle" scripts, then GUI fuses (only with bands and freezes of good structures), then quake, then any other. If you loose your structure, you come back to an old save and you try something else.

Now for your point on small test puzzles with zero points, see the contest puzzles here:

Joined: 06/06/2013
Groups: Gargleblasters

Thanks Bruno :)
I will keep trying. May just work on some expired ones for a bit until I get better


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons