ArticleJournal of chemical theory and computation2023
Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Dual-Coordinate Relative Free Energy Simulations Using Machine-Learned Interatomic Potentials.Journal of chemical theory and computation · 2026Article
- Predicting Solvation Free Energies of Molecules and Ions via First-Principles and Machine-Learning Molecular Dynamics.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
- Architecture-Independent Absolute Solvation Free Energy Calculations with Neural Network Potentials.The journal of physical chemistry letters · 2025Article
- Leveraging Molecular Mechanics With the uESE Continuum Solvation Model for Efficient Solvation Free Energy Prediction: Impact of Conformation and Extensive Validation.Journal of computational chemistry · 2025Article
- Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials.Journal of chemical theory and computation · 2025Article
- Identification of the potential Pan-CDK antagonists: tracing the path of virtual screening and inhibitory activity on lung cancer cells.Molecular diversity · 2025Article
- ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation.Journal of chemical theory and computation · 2025Article
- Fine-tuning molecular mechanics force fields to experimental free energy measurements.bioRxiv : the preprint server for biology · 2025Article
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.Journal of chemical information and modeling · 2024Article
- Parishin B blocking TRIB3-AKT1 interaction inhibits breast cancer lung metastasis.Frontiers in pharmacology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
We recently introduced transformato, an open-source Python package for the automated setup of large-scale calculations of relative solvation and binding free energy differences. Here, we extend the capabilities of transformato to the calculation of absolute solvation free energy differences. After careful validation against the literature results and reference calculations with the PERT module of CHARMM, we used transformato to compute absolute solvation free energies for most molecules in the FreeSolv database (621 out of 642). The force field parameters were obtained with the program cgenff (v2.5.1), which derives missing parameters from the CHARMM general force field (CGenFF v4.6). A long-range correction for the Lennard-Jones interactions was added to all computed solvation free energies. The mean absolute error compared to the experimental data is 1.12 kcal/mol. Our results allow a detailed comparison between the AMBER and CHARMM general force fields and provide a more in-depth understanding of the capabilities and limitations of the CGenFF small molecule parameters.
Identifiers
What OpenQuestion holds
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.