Jupyter Notebook Protein MD Setup tutorial
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This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.
Parameters
Inputs
Parameters needed to configure the workflow:
- pdbCode: PDB code of the protein-ligand complex structure (e.g. 1AKI)
Outputs
Output files generated (named according to the input parameters given above):
-
output_md_gro: final structure of the MD setup protocol
-
output_md_trr: final trajectory of the MD setup protocol
-
output_md_cpt: final checkpoint file
-
output_gppmd_tpr: final tpr file
-
output_genion_top_zip: final topology of the MD system
Version History
Version 6 (latest) Created 4th Mar 2024 at 14:12 by Genís Bayarri
Update to BioBB 4.1.*
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Version-6bab3b25
Version 5 Created 26th Jul 2023 at 10:17 by Genís Bayarri
Fixed importlib_metadata bug
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Version-5
f86759d
Version 4 Created 13th Apr 2023 at 16:35 by Genís Bayarri
Update to BioBB 4.0.*
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Version-4
efc1897
Version 3 Created 15th Sep 2022 at 10:24 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 77a78a
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Version-3
471a68f
Version 2 Created 1st Jul 2021 at 15:51 by Douglas Lowe
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Version-2
d4040dc
Version 1 (earliest) Created 7th May 2021 at 14:51 by Douglas Lowe
Uses GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit a81b483
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Views: 6407 Downloads: 1309
Created: 7th May 2021 at 14:51
Last updated: 13th Apr 2023 at 16:40
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Tutorials for BioEx...
Interactive Jupyter...
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.
Maintainers: Douglas Lowe, Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Pau Andrio
Number of items: 5
Tags: Not specified
Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
