Jupyter Notebook Classical Molecular Interaction Potentials
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Download RO-CrateCMIP MD Setup tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), and a MD simulation of the complex formed by the SARS-CoV-2 Receptor Binding Domain and the human Angiotensin Converting Enzyme 2 (PDB code 6VW1).
The code wrapped is the Classical Molecular Interaction Potentials (CMIP) code:
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins. Gelpí, J.L., Kalko, S.G., Barril, X., Cirera, J., de la Cruz, X., Luque, F.J. and Orozco, M. (2001) Proteins, 45: 428-437. https://doi.org/10.1002/prot.1159
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) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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Version 3 (latest) Created 6th Aug 2025 at 11:25 by Genís Bayarri
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Version 1 (earliest) Created 4th Mar 2024 at 14:46 by Genís Bayarri
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Views: 3244 Downloads: 1565
Created: 4th Mar 2024 at 14:46
Last updated: 6th Aug 2025 at 11:28
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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.
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