Docker Classical Molecular Interaction Potentials
Version 1

Workflow Type: Docker
Stable

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 22nd Apr 2024 at 11:28 by Genís Bayarri

Initial commit


Frozen Version-1 863d217
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2024). Docker Classical Molecular Interaction Potentials. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.820.1
Activity

Views: 628   Downloads: 432

Created: 22nd Apr 2024 at 11:28

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 10.5 MB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH