Jupyter Notebook Protein MD Setup tutorial
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Download RO CrateProtein MD Setup tutorial using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial.
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).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 3 (latest) 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-3471a68f
Version 2 Created 1st Jul 2021 at 15:51 by Douglas Lowe
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Version-2
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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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Creators and SubmitterViews: 2236
Created: 7th May 2021 at 14:51
Last updated: 17th Mar 2022 at 09:01
Last used: 5th Dec 2022 at 08:31
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Teams: BioBB Building Blocks
Organizations: The University of Manchester
https://orcid.org/0000-0002-1248-3594
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.
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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/
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.
