ArticleJournal of chemical theory and computation2025
Convergent Protocols for Computing Protein-Ligand Interaction Energies Using Fragment-Based Quantum Chemistry.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Energy-Screened Many-Body Expansion for Protein-Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven-Body Interactions.Journal of chemical theory and computation · 2026Article
- Accurate and Rapid Ranking of Protein-Ligand Binding Affinities Using Density Matrix Fragmentation and Physics-Informed Machine Learning Dispersion Potentials.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Analyzing Many-Body Charge Transfer Effects With the Fragment Molecular Orbital Method.Journal of computational chemistry · 2025Article
- Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.Journal of chemical theory and computation · 2025Article
- Quick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry.Journal of chemical information and modeling · 2025Article
- Fragme∩t: An Open-Source Framework for Multiscale Quantum Chemistry Based on Fragmentation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Fragment-based quantum chemistry methods offer a means to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein-ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing
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Registered trials
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