famp 0.0.3

FAMP - FRET assisted modeling Pipeline for RNA structures

The Project

This project combines different tools for modeling and simulation of RNA structures. Furthermore, functionalities were developed to efficiently analyze MD trajectories of labeled RNA. Here, the simulation of FRET experiments plays an essential role. Using the pipeline described here, RNA structures can be modeled and evaluated using smFRET experimental data.

Installation

You can set up FAMP in two different ways, depending on how much control you want over the environment:

1. Manual installation

   • Maximum freedom to choose your own versions of ViennaRNA, Rosetta, GROMACS and other tools/drivers.
   • Be aware: leaving out certain dependencies may limit functionality.

2. Build your own Docker image from our Dockerfile instructions with and without GPU support

   • Requires building the Docker Container, but keeps setup reproducible.

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Get the source code

You can download the source via the green “Code” button above or clone it directly from the terminal:

git clone https://github.com/BoernerLab/FAMP_rna.git

Requirements

As a dependency of this notebook the following programms should be preinstalled. Please follow the installation instructions of the tools.

ViennaRNAPackge

Rosetta

GROMACS

Make sure that the programms are added to the bashrc or zshrc file.

Please create an anaconda environment for this Jupyter Notebook by importing the environment.yml file.

Before you start open Pymol in your environment and install the plugins FRETraj and FRETlabel. Locate the package with fretlabel --path and remember this path. Then open PymMol and go to Plugin -> Plugin manager -> Install New Plugin -> Choose file ... -> and select fretlabel_gui.py, wich can be found at the path from the step bevore. The same works for the FRETraj GUI.

Author

Felix Erichson | erichson(at)hs-mittweida.de