{
  "abstract": "The ModCRElib package provides various tools for the analysis and modelling of transcription factor (TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF-binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF-binding sites, and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide five example uses of ModCRElib. This includes (i) TF-binding affinity prediction, (ii) TF ensemble pattern of bindings (aggregation of motifs), (iii) characterization of specificity in TF-binding sites along target DNA sequences, (iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Medicine and Life Sciences, (Structural Bioinformatics Group-GRIB), Universitat Pompeu Fabra , Barcelona, Catalonia 08003 ,",
    "Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver, BC V5Z 4H4 ,",
    "Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , Brno 625 00 ,",
    "International Clinical Research Center, St Anne’s University Hospital Brno , Brno 656 916 ,",
    "Biophysics in Cell Biology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra , Barcelona, Catalonia 08005 ,",
    "Institute of Biological, Environmental and Rural Science, Aberystwyth University , Aberystwyth SY23 3DA ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 11,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Patrick Gohl"
    },
    {
      "affs": [
        1
      ],
      "name": "Oriol Fornes",
      "orcid": "0000-0001-7479-2563"
    },
    {
      "affs": [
        0
      ],
      "name": "Patricia M Bota"
    },
    {
      "affs": [
        0
      ],
      "name": "Alberto Meseguer"
    },
    {
      "affs": [
        0
      ],
      "name": "Jaume Bonet"
    },
    {
      "affs": [
        0
      ],
      "name": "Ruben Molina-Fernández"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Joan Planas-Iglesias"
    },
    {
      "affs": [
        4
      ],
      "name": "Altair C Hernández"
    },
    {
      "affs": [
        4
      ],
      "name": "Oriol Gallego"
    },
    {
      "affs": [
        0,
        5
      ],
      "name": "Narcis Fernandez-Fuentes",
      "orcid": "0000-0002-6421-1080"
    },
    {
      "affs": [
        0
      ],
      "name": "Baldomero Oliva",
      "orcid": "0000-0003-0702-0250"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ej5fsnfq127tt.bib",
  "cited_by": 0,
  "doi": "10.1093/nargab/lqag122",
  "fulltext_url": "https://europepmc.org/articles/PMC13684267",
  "id": "ej5fsnfq127tt",
  "issns": [
    "2631-9268"
  ],
  "landing_url": "https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag122/8960102",
  "language": "eng",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7223148851",
  "pdf_url": "https://academic.oup.com/nargab/article-pdf/8/4/lqag122/72219631/lqag122.pdf",
  "pmcid": "PMC13684267",
  "pmid": "42909365",
  "published": "2026-10-21",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/ej5fsnfq127tt.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:39Z",
      "native_id": "10.1093/nargab/lqag122",
      "source": "crossref",
      "url": "https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag122/8960102"
    },
    {
      "first_seen": "2026-10-30T12:20:10Z",
      "native_id": "MED:42909365",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42909365"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "ModCRElib: a standalone package to model cis -regulatory elements",
  "title_text": "ModCRElib: a standalone package to model cis -regulatory elements",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:20:10Z",
  "url": "https://research.draconitic.com/paper/ej5fsnfq127tt",
  "venue": "NAR Genomics and Bioinformatics",
  "versions": []
}