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Macromolecular Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)

Based on the FlexServ server: 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 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).

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

PCA suite: 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

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


Settings

Biobb modules used

  • biobb_flexserv: biomolecular flexibility studies on protein 3D structures.

  • biobb_io: Tools to fetch biomolecular data from public databases.

  • biobb_structure_utils: Tools to modify or extract information from a PDB structure.

  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Auxiliar libraries used

  • jupyter: Free software, open standards, and web services for interactive computing across all programming languages.

  • plotly: Python interactive graphing library integrated in Jupyter notebooks.

  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

Take into account that, for this specific workflow, there are two environment files, one for linux OS and the other for mac OS:

linux

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

macos

git clone https://github.com/bioexcel/biobb_wf_flexserv.git
cd biobb_wf_flexserv
conda env create -f conda_env/environment.macos.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

Click here to execute tutorial in Binder


Version

2023.3 Release