Movers for Initialization, Sampling, etc (RosettaMP)

Table of Contents

Overview

The RosettaMP framework supports a set of movers that initialize elements of RosettaMP and implement sampling movers that account for the membrane environment. Each mover currently in the code and supported by the RosettaScripts interface is detailed in the pages below:

Movers for Initialization

AddMembraneMover Initialize the RosettaMP framework by adding a membrane representation to the pose
SymmetricAddMembraneMover Initialize the RosettaMP framework with a symmetric pose
AddMPLigandMover Add a single ligand to a pose already supported by the RosettaMP framework

Movers for changing the membrane position

MembranePositionFromTopology Calculate the membrane position from the transmembrane spans
SetMembranePositionMover Set the membrane position to a given center and normal
RandomMembranePositionMover Sample a random membrane position
FlipMover Reflect the pose about the xy plane of the membrane
TiltMover Tilts a single span or partner relative to the jump number
SpinAroundPartnerMover Spin the protein around the second partner in the xy plane
OptimizeMembranePositionMover Optimize the position of the membrane by deterministic search (relies on the scoring function)

Movers for docking

MPDockingMover Docks two membrane proteins
MPDockingSetupMover Reads in 2 poses and 2 spanfiles, concatenates them, and prints them out. Currently only works for 2 poses

Movers for sampling the protein embedding

TransformIntoMembraneMover Transform the protein into membrane coordinates
TranslationRotation Translate & rotate the protein from an old center/normal into a new center/normal
OptimizeProteinEmbeddingMover Optimizes the protein embedding in the membrane.

Movers for Visualization

VisualizeEmbeddingMover Add embedding residues to the pose to visualize embedding of spans, chains or the entire protein
VisualizeMembrane Add a series of pseudoatoms for visualizing the membrane as planes of pseudoatoms in visualization programs (very expensive)

Other Movers

MPLipidAccessibilityMover Computes which residues are lipid accessible and puts that information into the B-factors.
RangeRelaxMover Relaxes a membrane protein by relaxing iteratively in ranges.

References

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).

Contact

Rebecca Alford (rfalford12@gmail.com)
Julia Koehler Leman (julia.koehler1982@gmail.com)
Corresponding PI: Jeffrey J. Gray (jgray@jhu.edu)