{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      },
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/crate/1.1"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
        }
      ]
    },
    {
      "@id": "ro-crate-preview.html",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      }
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "mainEntity": {
        "@id": "biobb_wf_cmip.ipynb"
      },
      "datePublished": "2026-03-24 16:43:19 +0000",
      "author": [
        {
          "@id": "https://orcid.org/0000-0002-8291-8071"
        },
        {
          "@id": "https://orcid.org/0000-0003-0513-0288"
        }
      ],
      "license": "Apache-2.0",
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.773.4",
      "url": "https://workflowhub.eu/workflows/773/ro_crate?version=4",
      "name": "Research Object Crate for Jupyter Notebook Classical Molecular Interaction Potentials",
      "description": "# CMIP tutorial using BioExcel Building Blocks (biobb)\n\n***\n\nThis 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)).\n\nThe code wrapped is the ***Classical Molecular Interaction Potentials (CMIP)*** code:\n\n**Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins.**\n*Gelpí, J.L., Kalko, S.G., Barril, X., Cirera, J., de la Cruz, X., Luque, F.J. and Orozco, M. (2001)*\n*Proteins, 45: 428-437. [https://doi.org/10.1002/prot.1159](https://doi.org/10.1002/prot.1159)*\n\n***\n\n## Copyright &amp; Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) &amp; [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)).\n\n* (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")",
      "isBasedOn": "https://github.com/bioexcel/biobb_wf_cmip",
      "sdDatePublished": "2026-06-06 05:25:47 +0100",
      "creativeWorkStatus": "Stable",
      "hasPart": [
        {
          "@id": "biobb_wf_cmip.ipynb"
        },
        {
          "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.pdb"
        },
        {
          "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.top"
        },
        {
          "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/boxed_RBD-hACE2-ZN.pdb"
        },
        {
          "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/grid2.png"
        },
        {
          "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/conda_env/environment.yml"
        }
      ]
    },
    {
      "@id": "biobb_wf_cmip.ipynb",
      "@type": [
        "File",
        "SoftwareSourceCode",
        "ComputationalWorkflow"
      ],
      "url": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/biobb_wf_cmip.ipynb",
      "contentSize": 81314,
      "programmingLanguage": {
        "@id": "#jupyter"
      },
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/"
      },
      "description": "# CMIP tutorial using BioExcel Building Blocks (biobb)\n\n***\n\nThis 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)).\n\nThe code wrapped is the ***Classical Molecular Interaction Potentials (CMIP)*** code:\n\n**Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins.**\n*Gelpí, J.L., Kalko, S.G., Barril, X., Cirera, J., de la Cruz, X., Luque, F.J. and Orozco, M. (2001)*\n*Proteins, 45: 428-437. [https://doi.org/10.1002/prot.1159](https://doi.org/10.1002/prot.1159)*\n\n***\n\n## Copyright &amp; Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) &amp; [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)).\n\n* (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")",
      "name": "Jupyter Notebook Classical Molecular Interaction Potentials",
      "keywords": "",
      "version": 4,
      "license": "https://spdx.org/licenses/Apache-2.0",
      "creator": [
        {
          "@id": "https://workflowhub.eu/people/57"
        },
        {
          "@id": "https://workflowhub.eu/people/47"
        }
      ],
      "producer": {
        "@id": "https://workflowhub.eu/projects/11"
      },
      "dateCreated": "2026-03-24T16:41:06Z",
      "dateModified": "2026-05-13T13:04:25Z",
      "isPartOf": {
        "@id": "https://workflowhub.eu/collections/19"
      },
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.773.4",
      "isBasedOn": "https://workflowhub.eu/workflows/773?version=3",
      "input": [

      ],
      "output": [

      ],
      "sdPublisher": {
        "@id": "https://about.workflowhub.eu/"
      }
    },
    {
      "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.pdb",
      "@type": "File"
    },
    {
      "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/RBD-hACE2-ZN.top",
      "@type": "File"
    },
    {
      "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/boxed_RBD-hACE2-ZN.pdb",
      "@type": "File"
    },
    {
      "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/biobb_wf_cmip/notebooks/Files/grid2.png",
      "@type": "File"
    },
    {
      "@id": "https://github.com/bioexcel/biobb_wf_cmip/blob/main/conda_env/environment.yml",
      "@type": "File"
    },
    {
      "@id": "https://orcid.org/0000-0002-8291-8071",
      "@type": "Person",
      "name": "Adam Hospital",
      "identifier": "https://orcid.org/0000-0002-8291-8071"
    },
    {
      "@id": "https://orcid.org/0000-0003-0513-0288",
      "@type": "Person",
      "name": "Genís Bayarri",
      "identifier": "https://orcid.org/0000-0003-0513-0288"
    },
    {
      "@id": "https://workflowhub.eu/people/57",
      "@type": "Person",
      "name": "Adam Hospital"
    },
    {
      "@id": "https://workflowhub.eu/people/47",
      "@type": "Person",
      "name": "Genís Bayarri"
    },
    {
      "@id": "https://workflowhub.eu/projects/11",
      "@type": [
        "Project",
        "Organization"
      ],
      "name": "BioBB Building Blocks"
    },
    {
      "@id": "https://workflowhub.eu/collections/19",
      "@type": "Collection",
      "name": "Interactive Jupyter Notebooks for FAIR and reproducible biomolecular simulation workflows"
    },
    {
      "@id": "#jupyter",
      "@type": "ComputerLanguage",
      "name": "Jupyter",
      "identifier": {
        "@id": "https://jupyter.org/"
      },
      "url": {
        "@id": "https://jupyter.org/"
      }
    },
    {
      "@id": "https://about.workflowhub.eu/",
      "@type": "Organization",
      "name": "WorkflowHub",
      "url": "https://about.workflowhub.eu/"
    }
  ]
}