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  "_id": "6ab63a2b99f7aa8c6aa2c88a",
  "Package": "MDaRes",
  "Title": "MD Analysis of Residue Properties Using Structural Alphabets",
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  "Authors@R": "c(\nperson(given = \"Nancy\",\nfamily = \"D'Arminio\",\nrole = c(\"aut\"),\nemail = \"nancydarminio67@gmail.com\",\ncomment = c(ORCID = \"0000-0002-8065-2142\")),\nperson(given = \"Anna\",\nfamily = \"Marabotti\",\nrole = \"aut\",\nemail = \"amarabotti@unisa.it\",\ncomment = c(ORCID = \"0000-0002-9510-5205\")),\nperson(given = \"Alessandro\",\nfamily = \"Pandini\",\nrole = c(\"aut\", \"cph\", \"cre\"),\nemail = \"alessandro.pandini@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4158-233X\"))\n)",
  "Description": "Analyze molecular dynamics (MD) simulation data using\nstructural alphabets. Protein local conformations from\nmolecular simulations are encoded in a compressed string\nrepresentation. Residue-level UniProt annotations can be\ndirectly retrieved. Comparative analysis tools are available to\ninvestigate conformational variability, coordinated motions,\nand differences between systems (e.g. wild-type vs mutant;\nbound vs unbound). Methodological details for the structural\nalphabet analysis can be found in Pandini et al. (2013)\n<doi:10.1093/bioinformatics/btt326>.",
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  "Author": "Nancy D'Arminio [aut] (ORCID:\n<https://orcid.org/0000-0002-8065-2142>), Anna Marabotti [aut]\n(ORCID: <https://orcid.org/0000-0002-9510-5205>), Alessandro\nPandini [aut, cph, cre] (ORCID:\n<https://orcid.org/0000-0002-4158-233X>)",
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  "Repository": "https://alepandini.r-universe.dev",
  "Date/Publication": "2026-08-25 15:10:09 UTC",
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    "add_disulfide_bond",
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    "add_glycosilation",
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      "page": "add_active_site",
      "title": "Retrieve and Format Active Site Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_binding_site",
      "title": "Retrieve and Format Ligand Binding Site Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_disulfide_bond",
      "title": "Retrieve and Format Disulfide Bond Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_domain",
      "title": "Retrieve and Format Domain Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_glycosilation",
      "title": "Retrieve and Format Glycosylation Annotations from UniProt",
      "topics": [
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      ]
    },
    {
      "page": "add_lipidation",
      "title": "Retrieve and Format Lipidation Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_location",
      "title": "Retrieve and Format Location Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_modified_residue",
      "title": "Retrieve and Format Modified Residue Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_molecule_processing",
      "title": "Retrieve and Format Molecule Processing Annotations from UniProt",
      "topics": [
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      ]
    },
    {
      "page": "add_motive",
      "title": "Retrieve and Format Motif Annotations from UniProt",
      "topics": [
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    },
    {
      "page": "add_secondary_structure",
      "title": "Retrieve and Format Secondary Structure Annotations from UniProt",
      "topics": [
        "add_secondary_structure"
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    },
    {
      "page": "add_uniprot_annotation",
      "title": "Retrieve and Merge UniProt Annotations",
      "topics": [
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    },
    {
      "page": "add_variants",
      "title": "Retrieve and Format Protein Variants from UniProt",
      "topics": [
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    },
    {
      "page": "colnames_substring",
      "title": "Extract Substring from Column Names",
      "topics": [
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    },
    {
      "page": "create_annotation_df",
      "title": "Retrieve UniProt Protein Sequence and Format as Dataframe",
      "topics": [
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    },
    {
      "page": "do_freq_diff_plot",
      "title": "Save frequency-difference plot to PNG",
      "topics": [
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    },
    {
      "page": "do_freq_plot",
      "title": "Generate Frequency Profile Plot and Save to PNG",
      "topics": [
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    },
    {
      "page": "do_MI_plot",
      "title": "Generate Mutual Information Matrix Plot and Save to PNG",
      "topics": [
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    },
    {
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      "title": "Save Shannon Entropy Difference Plot to PNG",
      "topics": [
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    {
      "page": "do_shannon_entropy_plot",
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      "topics": [
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    },
    {
      "page": "entropy_visualization",
      "title": "Visualize Shannon Entropy on a Protein Structure",
      "topics": [
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    },
    {
      "page": "freq_diff_plot",
      "title": "Plot Structural Frequency Differences",
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      "topics": [
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    {
      "page": "get_res_numbering",
      "title": "Retrieve Residue Numbering from Encoded Trajectory",
      "topics": [
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      "title": "Import Structural Alphabet from PDB Files",
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    {
      "page": "MI_plot",
      "title": "Plot Mutual Information Matrix",
      "topics": [
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    },
    {
      "page": "MI_ranking_couple",
      "title": "Rank Residues Based on Mutual Information",
      "topics": [
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      "title": "Rank Mutual Information by Median and Collectivity",
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