# Research Object Crate for Apache Airflow Classical Molecular Interaction Potentials

Original URL: https://workflowhub.eu/workflows/2157/ro_crate?version=1

# 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) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2026 [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
  Genís Bayarri, Adam Hospital
License
  Apache-2.0

## Contents

Main Workflow: Apache Airflow Classical Molecular Interaction Potentials
Size: 6622 bytes
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/README.md
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/acpype_params_ac.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/amber_to_pdb.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cat_pdb.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cmip_ignore_residues.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cmip_prepare_pdb.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cmip_prepare_structure.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cmip_run.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/cmip_titration.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/extract_chain.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/extract_heteroatoms.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/leap_gen_top.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/reduce_add_hydrogens.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/remove_ligand.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/remove_pdb_water.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/biobb_adapters/sander_mdrun.cwl
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/Files/RBD-hACE2-ZN.pdb
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/Files/RBD-hACE2-ZN.top
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/complex.pdb
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step0_cmip_prepare_pdb.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step10_leap_gen_top.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step11_sander_mdrun.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step12_amber_to_pdb.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step13_cmip_prepare_structure.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step14_remove_ligand.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step15_cmip_ignore_residues.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step16_cmip_run_int_en.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step17_cmip_prepare_structure.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step18_extract_chain_a.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step19_extract_chain_b.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step1_cmip_titration.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step20_cmip_run_rbd.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step21_cmip_run_hace2.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step22_cmip_run_rbd_hace2.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step23_cmip_ignore_residues_rbd.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step24_cmip_run_prot_prot.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step25_cmip_ignore_residues_hace2.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step26_cmip_run_complex.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step2_cat_pdb.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step3_cmip_run_pos.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step4_cmip_run_neg.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step5_cmip_run_neu.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step6_remove_pdb_water.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step7_extract_heteroatoms.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step8_reduce_add_hydrogens.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/step9_acpype_params_ac.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_cmip/airflow/inputs/structure.pdb