{
  "abstract": "GroScore is an open-source Python toolkit that automates the scoring of protein–protein structures using bidirectional steered molecular dynamics (SMD) simulations with explicit solvent. Building on a previously published unidirectional pulling approach, the current version introduces bidirectional pulling (unbinding and rebinding), interface cutout for reduced computational cost, support for three force fields (AMBER19SB, CHARMM36m, GROMOS 54A8), and automated handling of small molecules and noncanonical amino acids (using OpenFF), structural ions, and crystal waters. GroScore integrates with GROMACS and SLURM for high-performance computing and is validated on protein–protein affinity benchmarks, showing significant correlation between computed scores and experimental binding affinities across all tested force fields. The software is freely available at https://github.com/jwperthold/GroScore under the MIT License.",
  "abstract_shown": true,
  "affiliations": [
    "Independent Researcher, Vienna 1130, Austria",
    "Institute for Molecular Modeling and Simulation, Department of Natural Sciences and Sustainable Resources, BOKU University, Muthgasse 18, Vienna 1190, Austria",
    "Christian Doppler Laboratory for Molecular Informatics in the Biosciences, BOKU University, Muthgasse 18, Vienna 1190, Austria"
  ],
  "article_type": "brief report",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jan Walther Perthold",
      "orcid": "0000-0002-8575-0278"
    },
    {
      "affs": [
        1
      ],
      "name": "Dražen Petrov",
      "orcid": "0000-0001-6221-7369"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Chris Oostenbrink",
      "orcid": "0000-0002-4232-2556"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ds7vcgmy59255.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jcim.6c01771",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13715378/",
  "id": "ds7vcgmy59255",
  "issns": [
    "1549-9596",
    "1549-960X"
  ],
  "landing_url": "https://doi.org/10.1021/acs.jcim.6c01771",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Application Note"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7216081901",
  "pdf_url": "https://pubs.acs.org/jcisd8/article-pdf/doi/10.1021/acs.jcim.6c01771/68738808/acs.jcim.6c01771.pdf",
  "pmcid": "PMC13715378",
  "pmid": "42929558",
  "published": "2026-10-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ds7vcgmy59255.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T12:22:42Z",
      "native_id": "PMC13715378",
      "source": "pmc",
      "url": "https://doi.org/10.1021/acs.jcim.6c01771"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "GroScore: Automated Scoring of Protein–Protein Interactions Using Bidirectional Steered Molecular Dynamics",
  "title_text": "GroScore: Automated Scoring of Protein–Protein Interactions Using Bidirectional Steered Molecular Dynamics",
  "type": "peer-reviewed",
  "updated_at": "2026-11-01T12:22:42Z",
  "url": "https://research.draconitic.com/paper/ds7vcgmy59255",
  "venue": "Journal of Chemical Information and Modeling",
  "versions": []
}