Last Modified: 5/22/2014
The Rosetta low resolution (centroid-based) energy function for membrane proteins was developed in 2006 with the Membrane Ab Initio folding protocol (Yarov-Yaravoy et al. 2006). It was derived from 28 alpha helical membrane proteins and is knowledge-based. There are 6 low-resolution energy terms: a residue-environment energy, residue-residue energy, packing density, termini penalty, non helix penalty, and tm projection penalty.
Terms supported by the RosettaMembrane framework were added in April 2014. Terms, corresponding energy methods, and usage are described below. The score name is the name of the term you would use when setting up a weights file.
Score Name: MPEnv. Score per-residue interactions with the membrane environment using a 5 layer membrane (Layers: inner hydrophobic, outer hydrophobic, interface, polar, water). Energy Method type: One body context-dependent. For Developers - code in core/scoring/membrane/MPEnvEnergy.hh.
Score Name: MPPair. Score residue-residue interactions in the membrane environment using a 2 layer membrane (Layers: hydrophobic, polar). Energy Method Type: Two-body context dependent. For Developers - code in core/scoring/membrane/MPPairEnergy.hh
Score Name: MPCBeta. Score packing-density in the membrane based on the number of helices. Energy Method Type: One Body context dependent. For Developers - code in core/scoring/membrane/MPCbetaEnergy.hh
Score Name: MPTermini. Penalty for termini residues (N- or C- termini) in the membrane. Energy Method Type: Whole structure energy. For Developers - code in /core/scoring/membrane/MPTerminiPenalty.hh
Score Name: MPTMProj. Penalty for helices longer than thickness of the membrane. Energy Method type: Whole Structure Energy. For Developers - code in core/scoring/membrane/MPTMProjPenalty.hh
Score Name: MPNonHelix. Penalty for non helix residues in the membrane. Uses Secondary structure in Rosetta (or provided). Energy Method Type: One body context independent energy. For Developers - code in core/scoring/membrane/MPNonHelixPenalty.hh
| Option Name | Description | Type |
|---|---|---|
| score:find_neighbors_3dgrid | Use 3D lookup table in neighbor calculations | boolean |
| membrane:no_interpolate_Mpair | switch off interpolation between 2 layers when a pair of residues is on the boundary | boolean |
The set of terms described above are only for use with the new membrane framework protocols. The old set of energy terms can be found in core/scoring/methods.
Yarov-Yarovoy V, Schonbrun J, Baker D. (2006 Mar 1) Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4):1010-25.