Code and Demo

This application uses Movers from RosettaMP. The score_jd2 application can be found at public/analysis/score_jd2.cc. The supplement of the manuscript below also outlines its use.

Algorithm Description

Scoring a membrane protein with a defined score function is one of the most basic and much needed functionality. For this, we hijacked the score_jd2 application and made it (at least partly) applicable for membrane proteins.

Rosetta Revision #58096

Run the application

There are two modes available for this application:

1) Having a fixed membrane and a fixed protein. This scores the protein as is and requires that the protein is already transformed into membrane coordinates (see PDB-file on how to do this) and currently only works if a spanfile is given, which can be generated from the transformed structure (see the MPSpanfileFromPDB application). Example flags:

Rosetta/main/source/bin/score_jd2.macosclangrelease \
-database Rosetta/main/database \
-in:file:s 1AFO_tr.pdb \
-in:membrane \
-mp:setup:spanfiles 1AFO__tr.span \
-score:weights mpframework_smooth_fa_2012.wts \

2) Having a fixed membrane a movable protein. This transforms the protein into membrane coordinates first before it is scored. It does not require the protein to be transformed into membrane coordinates and works with a regular cleaned PDB file. However, it requires a spanfile as input. Example flags:

Rosetta/main/source/bin/score_jd2.macosclangrelease \
-database Rosetta/main/database \
-in:file:s 1AFO.pdb \
-in:membrane \
-mp:setup:spanfiles 1AFO__tr.span \
-mp:setup:transform_into_membrane \
-score:weights mpframework_smooth_fa_2012.wts \

Both applications only score the protein and don't optimize the membrane position with the scorefunction! Use the flags in the next section to change settings. Note: Make sure your numbering between PDB file and spanfile match!

Flags / Options

Flag Description
-mp::setup::transform_into_membrane <bool> Required to score membrane proteins. Add this option to transform the protein pose into the membrane.
-mp::transform::optimize_embedding <bool> Use the scorefunction to optimize the embedding after an initial coarse grained setting.

Citation

Alford RF, Koehler Leman J, Weitzner BD, Duran A, Tiley DC, Gray JJ (2015). An integrated framework advancing membrane protein modeling and design. PLoS Comput. Biol; 11(9).

Koehler Leman J, Mueller BK, Gray JJ (2017). Expanding the toolkit for membrane protein modeling in Rosetta. Bioinformatics; 33(5).

Contact

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