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.
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
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!
| 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. |
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).
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