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[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_pmx_tutorial/HEAD?labpath=biobb_wf_pmx_tutorial%2Fnotebooks%2Fbiobb_wf_pmx_tutorial.ipynb)


# Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)

***

**Based on the official [pmx tutorial](http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/index.html).**

***

This tutorial aims to illustrate how to compute a **fast-growth mutation free energy** calculation, step by step, using the BioExcel **Building Blocks library (biobb)**. The particular example used is the **Staphylococcal nuclease** protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

The **non-equilibrium free energy calculation** protocol performs a **fast alchemical transition** in the direction **WT->Mut** and back **Mut->WT**. The two equilibrium trajectories needed for the tutorial, one for **Wild Type (WT)** and another for the **Mutated (Mut)** protein (Isoleucine 10 to Alanine -I10A-), have already been generated and are included in this example. We will name **WT as stateA** and **Mut as stateB**.

![](https://raw.githubusercontent.com/bioexcel/biobb_wf_pmx_tutorial/master/biobb_wf_pmx_tutorial/notebooks/schema.png)

The tutorial calculates the **free energy difference** in the folded state of a protein. Starting from **two 1ns-length independent equilibrium simulations** (WT and mutant), snapshots are selected to start **fast (50ps) transitions** driving the system in the **forward** (WT to mutant) and **reverse** (mutant to WT) directions, and the **work values** required to perform these transitions are collected. With these values, **Crooks Gaussian Intersection** (CGI), **Bennett Acceptance Ratio** (BAR) and **Jarzynski estimator** methods are used to calculate the **free energy difference** between the two states.

*Please note that for the sake of disk space this tutorial is using 1ns-length equilibrium trajectories, whereas in the [original example](http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/eq.mdp) the equilibrium trajectories used were obtained from 10ns-length simulations.*

***

## Settings

### Biobb modules used

* [biobb_pmx](https://github.com/bioexcel/biobb_pmx): Tools to setup and run Alchemical Free Energy calculations.
* [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations.
* [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories.

### Auxiliary libraries used

* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
* [plotly](https://plot.ly/python/offline/): Python interactive graphing library integrated in Jupyter notebooks.

### Conda Installation and Launch

```console
git clone https://github.com/bioexcel/biobb_wf_pmx_tutorial.git
cd biobb_wf_pmx_tutorial
conda env create -f conda_env/environment.yml
conda activate biobb_wf_pmx_tutorial
jupyter-notebook biobb_wf_pmx_tutorial/notebooks/biobb_wf_pmx_tutorial.ipynb
```

***

## Tutorial

Click here to [view tutorial in Read the Docs](https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/?badge=latest)

Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_pmx_tutorial/HEAD?labpath=biobb_wf_pmx_tutorial%2Fnotebooks%2Fbiobb_wf_pmx_tutorial.ipynb)

***

## Version
2024.1

## Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).

* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)

Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")