Work

Atomic Decomposition and Mapping of Solute Thermodynamics

Year: 2026

Type: preprint

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.

Source: ChemRxiv

DOI: 10.26434/chemrxiv.15008034/v1

Authors: Joe Cruz, Samrat Lohar, Helmut Carter, Steven Ramsey, Daniel R. Roe, Michael K. Gilson, Tom Kurtzman

Institutions: Lehman College, City University of New York, National Institutes of Health, University of California San Diego, National Heart, Lung, and Blood Institute

Language: English

Topic: Computational Drug Discovery Methods

Subfield: Drug Discovery

Field: Pharmacology, Toxicology and Pharmaceutics

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7204828432

Cites:

Cited by: 1

Related to: 10