[](https://biobb-wf-flexserv.readthedocs.io/en/latest/?badge=latest)
[](https://mybinder.org/v2/gh/bioexcel/biobb_wf_flexserv/HEAD?labpath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynb)
[](https://colab.research.google.com/github/bioexcel/biobb_wf_flexserv/blob/main/biobb_wf_flexserv/notebooks/biobb_wf_flexserv.ipynb)
# Macromolecular Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
Based on the FlexServ server: [https://mmb.irbbarcelona.org/FlexServ/](https://mmb.irbbarcelona.org/FlexServ/)
***
This tutorial aims to illustrate the process of generating **protein conformational ensembles** from **3D structures** and analysing its **molecular flexibility**, step by step, using the **BioExcel Building Blocks library (biobb)**.
The notebook reproduces the workflow integrated in the **FlexServ** web-based tool for the analysis of **protein flexibility**. The workflow incorporates powerful protocols for the **coarse-grained** determination of **protein dynamics** using different versions of **Normal Mode Analysis (NMA)**, **Brownian dynamics (BD)** and **Discrete Molecular Dynamics (DMD)**. It also includes a set of **flexibility analyses** using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann’s indexes, dynamic domain determination, hinge point detections, etc. Data is represented using NGL 3D-structure visualizer and Plotly 2D plots.
The particular structure used is the **Ribosomal Protein S15 from Bacillus stearothermophilus** (PDB code [1A32](https://www.rcsb.org/structure/1A32)).
The codes wrapped are the ***FlexServ*** and ***PCAsuite*** tools:
**FlexServ: an integrated tool for the analysis of protein flexibility.**
*Bioinformatics, Volume 25, Issue 13, 1 July 2009, Pages 1709–1710.*
*Available at: [https://doi.org/10.1093/bioinformatics/btp304](https://doi.org/10.1093/bioinformatics/btp304)*
**PCA suite**: [https://mmb.irbbarcelona.org/software/pcasuite/](https://mmb.irbbarcelona.org/software/pcasuite/)
**Essential Dynamics: A Tool for Efficient Trajectory Compression and Management.**
*J. Chem. Theory Comput. 2006, 2, 2, 251–258*
*Available at: [https://doi.org/10.1021/ct050285b](https://doi.org/10.1021/ct050285b)*
**pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data.**
*SoftwareX, Volume 5, 2016, Pages 44-50*
*Available at: [https://doi.org/10.1016/j.softx.2016.04.002](https://doi.org/10.1016/j.softx.2016.04.002)*
***
## Settings
### Biobb modules used
* [biobb_flexserv](https://github.com/bioexcel/biobb_flexserv): biomolecular flexibility studies on protein 3D structures.
* [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch biomolecular data from public databases.
* [biobb_structure_utils](https://github.com/bioexcel/biobb_structure_utils): Tools to modify or extract information from a PDB structure.
* [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.
* [nglview](https://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
* [simpletraj](https://github.com/arose/simpletraj): Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
### Conda Installation and Launch
```console
git clone https://github.com/bioexcel/biobb_wf_flexserv.git
cd biobb_wf_flexserv
conda env create -f conda_env/environment.yml
conda activate biobb_wf_flexserv
jupyter-notebook biobb_wf_flexserv/notebooks/biobb_wf_flexserv.ipynb
```
***
## Tutorial
Click here to [view tutorial in Read the Docs](https://biobb-wf-flexserv.readthedocs.io/en/latest/tutorial.html)
Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_flexserv/HEAD?labpath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynb)
Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_flexserv/blob/main/biobb_wf_flexserv/notebooks/biobb_wf_flexserv.ipynb)
***
## Version
2025.1 Release
## 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.
