application_documentation/membrane_proteins/RosettaMP Movers OptimizeProteinEmbedding

Getting Started

Build Documentation

Rosetta Tutorials

Rosetta Basics

Rosetta Applications

• Structure Prediction

• Design

• Docking

• Analysis

• Utilities

• Antibody-specific applications

• RNA-specific applications

• Tools

• Full apps list

Rosetta Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

RosettaEncyclopedia

Options list

Metadata

Questions and comments to:

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

Last Updated: 2/8/18

Description

This Mover optimizes the protein embedding in the membrane given the smooth high-res score function; transforms the protein into the membrane, optimizes the membrane position (flexible), and uses the optimized embedding to reposition the protein in the membrane.

Code and Demo

The Mover lives in main/source/src/protocols/membrane/.

RosettaScripts interface

TODO: Currently not compatible with RosettaScripts.

Flags / Options

Flag	Description
-mp::transform::optimize_embedding <bool>	Use the scorefunction to optimize the embedding after an initial coarse grained setting.

Reference

RosettaMP is described in

• Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Elazar A, Tilley DC, Gray JJ (2015) An integrated framework advancing membrane protein modeling and design, PLoS Computational Biology (in press)