{
  "abstract": "Here we present theory, methods, and software that decomposes the free energy of a solvated solute into its energetic and entropic contributions and maps these quantities to solute atoms. Because the mapping is atomic, contributions can be summed over any set of atoms of interest, giving thermodynamic values for ligand functional groups, protein backbone and side chains, individual residues, or an entire binding site. Software implementing the energy decomposition is integrated into cpptraj in AmberTools and software introduced and described here. We illustrate the approach by atomistically mapping the energetic and entropic contributions of ligand 735 and of the binding-site residues of PPAR-α.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemistry, Lehman College4",
    "City University of New York",
    "National Heart, Lung, and Blood Institute",
    "National Institutes of Health",
    "Skaggs School of Pharmacy and Pharmaceutical Sciences",
    "University of California San Diego"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "name": "Joe Cruz"
    },
    {
      "name": "Samrat Lohar"
    },
    {
      "name": "Helmut Carter"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Steven Ramsey"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Daniel R. Roe"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Michael K. Gilson"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Tom Kurtzman",
      "orcid": "0000-0003-0900-772X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/57p176zrprqm3.bib",
  "cited_by": 1,
  "doi": "10.26434/chemrxiv.15008034/v1",
  "fulltext_url": null,
  "id": "57p176zrprqm3",
  "issns": [],
  "landing_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008034/v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1703|Computational Drug Discovery Methods"
    ]
  ],
  "openalex": "W7204828432",
  "pdf_url": "https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008034/v1",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-30",
  "publisher": "American Chemical Society (ACS)",
  "ris": "https://research.draconitic.com/paper/57p176zrprqm3.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:17Z",
      "native_id": "10.26434/chemrxiv.15008034",
      "source": "chemrxiv",
      "url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008034/v1"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "source:chemrxiv",
      "subfield": "general"
    }
  ],
  "title": "Atomic Decomposition and Mapping of Solute Thermodynamics",
  "title_text": "Atomic Decomposition and Mapping of Solute Thermodynamics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:17Z",
  "url": "https://research.draconitic.com/paper/57p176zrprqm3",
  "venue": "ChemRxiv",
  "versions": []
}