# Research Object Crate for Jupyter Notebook Classical Molecular Interaction Potentials

Original URL: https://workflowhub.eu/workflows/773/ro_crate?version=2

# 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](https://www.rcsb.org/structure/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](https://www.rcsb.org/structure/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](https://doi.org/10.1002/prot.1159)* *** ## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")

Author
  Adam Hospital, Genís Bayarri
License
  Apache-2.0

## Contents

Main Workflow: Jupyter Notebook Classical Molecular Interaction Potentials
Size: 78658 bytes
https://github.com/bioexcel/biobb_wf_cmip/blob/main/conda_env/environment.yml
https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.pdb
https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.top
https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/boxed_RBD-hACE2-ZN.pdb
https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/grid2.png