ArticleJournal of computational chemistry2022
Automation of AMOEBA polarizable force field for small molecules: Poltype 2.
Article in Journal of computational chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 60 citations in OpenAlex.
- Bridging quantum mechanics to liquid properties via a universal organic force field.Nature communications · 2026Article
- Article
- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models.Journal of chemical theory and computation · 2026Article
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations.Chemical & biomedical imaging · 2025Article
- Physics-Based Solubility Prediction for Organic Molecules.Chemical reviews · 2025Review
- Mitigating product inhibition in 2'-hydroxybiphenyl-2-sulfinate desulfinase (DszB) with synthetic glycosylation.Protein science : a publication of the Protein Society · 2025Article
- The Q-AMOEBA (CF) Polarizable Potential.The journal of physical chemistry letters · 2025Article
- Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?Journal of chemical information and modeling · 2025Review
- Soybean Lectin Cross-Links Membranes by Binding Sulfatide in a Curvature-Dependent Manner.Journal of agricultural and food chemistry · 2025Article
- Binding free energy analysis of galectin-3 natural ligands and synthetic inhibitors.Protein science : a publication of the Protein Society · 2025Article
- Streamlined Postprocessing of NMR Structures with the Molecular Restrainer: A Universal Tool for High-Quality Protein-Ligand Models and Non-Standard Amino Acid Residues.International journal of molecular sciences · 2025Article
- TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations.Journal of chemical theory and computation · 2025Article
- Modelling Lithium-Ion Transport Properties in Sulfoxides and Sulfones with Polarizable Molecular Dynamics and NMR Spectroscopy.ChemPlusChem · 2025Article
- Simulations of γ-Valerolactone Solvents and Electrolytes for Lithium Batteries Using Polarizable Molecular Dynamics.Molecules (Basel, Switzerland) · 2025Article
- Hydrogen Bond Blueshifts in Nitrile Vibrational Spectra Are Dictated by Hydrogen Bond Geometry and Dynamics.JACS Au · 2024Article
- A Polarizable Forcefields for Glyoxal Acetals as Electrolyte Components for Lithium-Ion Batteries.ChemistryOpen · 2024Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals.The Journal of chemical physics · 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 at 1 institution in 1 country.
Funding
Abstract
A next-generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non-aromatic ring torsion parameterization, coupled torsion-torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio-fragments such as amino and nucleic acids.
Indexed as
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.