application_documentation/membrane_proteins/RosettaMP Movers MPDockingSetup

Getting Started

Build Documentation

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Rosetta Basics

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• Structure Prediction

• Design

• Docking

• Analysis

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• Antibody-specific applications

• RNA-specific applications

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Rosetta Scripting Interfaces

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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 reads in 2 poses and 2 spanfiles, concatenates them, and prints them out. It currently only works for 2 poses.

Code and Demo

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

RosettaScripts interface

The following options are available within the RosettaScript interface:

optimize1 - bool - should the position of partner 1 be optimized in the membrane? optimize2 - bool - should the position of partner 2 be optimized in the membrane? pose1 - String - Provide the first pose. pose2 - String - Provide the second pose. span1 - String - Provide the first spanfile. span2 - String - Provide the second spanfile.

Flags / Options

Flag	Description
-mp::setup::optimize1 <Type>	Optimize partner 1 when intializing from cmd.
-mp::setup::optimize2 <Type>	Optimize partner 2 when intializing from cmd.

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)