ArticleJournal of computational chemistry2025
Evaluating the Functional Importance of Conformer-Dependent Atomic Partial Charge Assignment.
Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Identification of novel VPS4 inhibitors using multi-tiered structure based virtual screening.Molecular diversity · 2026Article
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- Machine-Learned Electrostatic Potentials for Accurate Hydration Free Energy Calculations.Journal of chemical theory and computation · 2026Article
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules.Journal of chemical theory and computation · 2025Article
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
- Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations.Journal of chemical information and modeling · 2025Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Physics-based methods such as protein-ligand binding free energy calculations have been increasingly adopted in early-stage drug discovery to prioritize promising compounds for synthesis. However, the accuracy of these methods is highly dependent on the details of the calculation and choices made while preparing the ligands and protein ahead of running calculations. During ligand preparation, researchers typically assign partial atomic charges to each ligand atom using a specific ligand conformation for charge assignment, often the input conformer. While it is a well-known problem that partial charge assignment is dependent on conformation, little investigation has explored the downstream effects of varied partial charge assignment on free energy estimates. Preliminary benchmarks from the Open Free Energy Project show that generating partial charges from different input conformers leads to variation of up to
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.