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Recipe: makehelix
Created by jeff101 91 193
Your rating: None Average: 4.8 (10 votes)


Name: makehelix
ID: 42111
Created on: Sat, 06/02/2012 - 13:53
Updated on: Sun, 06/03/2012 - 03:52

makes beta-sheets and different kinds of helices in a protein

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jeff101's picture
User offline. Last seen 19 hours 20 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

This recipe asks the user for two residue numbers and a secondary-structure type. It then adds bands to all residues between the two residue numbers to make that region of the protein change to the secondary-structure's conformation. It freezes all other parts of the protein and adds some anchor bands if the protein is more than one strand. Then it wiggles the protein. Ideally, the wiggling ends quickly, and then the recipe repeats, asking the user for new residue numbers and a new secondary-structure type.

When using this recipe, it often helps to vary the Clashing Importance to change the amount of time spent wiggling. You can also remove bands when the recipe pauses between user inputs. It also helps to run this recipe with residues colored by relative score. Then you can tell which regions are in the most unfavorable conformations (they will be red rather than green).

Right now, makehelix is coded to make beta-sheets and left- or right-handed alpha, 3-10, pi, or gamma helices. I would like to expand it to include 2.2-7 helices and different kinds of turns. If you know of references listing details (distances, angles) about these structures, please e-mail me about them.

Another feature that would help is better detection of strand breaks in the protein (like in puzzle 547). Right now, makehelix uses a distance cutoff to detect breaks. If you know of other ways to detect the ends of individual strands in the protein, please e-mail me about them.

If you have other suggestions for improvements to makehelix, please e-mail them to me. Most things can be improved, and the more complicated a piece of software is, the more likely it is to have bugs.

Joined: 09/24/2012
Groups: Go Science
It's more sophisticated than the new SS tool

I discover this recipe too late. I think than even after the new SS tool, it can be useful by allowing us to vary the helix structure (right handed left handed etc).
Thanks !

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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, RosettaCommons