Python Classical Molecular Interaction Potentials
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Workflow Type: Python
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CMIP 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).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Version History

Version 1 (earliest) Created 4th Mar 2024 at 15:04 by Genís Bayarri

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Hospital, A., & Bayarri, G. (2024). Python Classical Molecular Interaction Potentials. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.774.1
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Created: 4th Mar 2024 at 15:04

Last updated: 4th Mar 2024 at 15:07

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