Remix not remixing penult segment.

Case number:699969-2009808
Opened by:Serca
Opened on:Saturday, June 6, 2020 - 20:01
Last modified:Monday, June 8, 2020 - 11:10

We all know that Remix is not remixing protein endings.
The reason for that are the angles of amino acid connection. First residue has no any AA before itself, so no angle, and no solution on Remix on the 1st residue.
Same problem is for the last protein residue for the same reason.

But next one, the 2nd residue is pretty able to be remixed, because it has all the angles with both neighborhoods.

And here is the problem: Remix tool gives no solutions when penult protein residue is selected. And there is just no good reason for that. If 2nd residue could be remixed, penult residue has to be either.
I consider that a bug of the algorithm or its implementation.

Does Rosetta loophash has the same problem?

(Sat, 06/06/2020 - 20:01  |  2 comments)

agcohn821's picture
User offline. Last seen 11 hours 4 min ago. Offline
Joined: 11/05/2019
Groups: Foldit Staff


Hi Serca! Thank you for pointing out this concern--I have passed this along to our team.

Serca's picture
User offline. Last seen 2 years 1 week ago. Offline
Joined: 02/03/2020
Groups: Go Science

The reason for that could be the misinterpretation of the two zero angle records in the Remix backbone.db in the end of each protein.


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