Jupyter Notebook Protein Conformational Transitions calculations tutorial
View on GitHub
Download RO-CrateProtein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
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) 2015-2025 Barcelona Supercomputing Center
- (c) 2015-2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 3 (latest) Created 6th Aug 2025 at 12:39 by Genís Bayarri
Update to 5.1.*
Frozen
Version-3832d84b
Version 1 (earliest) Created 2nd Aug 2023 at 10:35 by Genís Bayarri
Initial commit
Frozen
Version-1
c92cc96
Creators and Submitter
Views: 4609 Downloads: 1472
Created: 2nd Aug 2023 at 10:35
Last updated: 6th Aug 2025 at 12:41
TagsThis item has not yet been tagged.
AttributionsNone
Collections
Interactive Jupyter...
Related items
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 ...
