Skip to content
Log in
Sponsored AI Networking Cookbook: Practical recipes for AI-assisted network automation and development AI Networking Cookbook: Practical recipes for AI-assisted network automation and development

Similar papers

Preprint Aug 2026

Evaluating Electrostatic Embedding MLIP/MM for Relative Binding Free Energy Calculations

Electrostatic embedding improved every accuracy and correlation metric for TYK2 but performed comparably to the classical and mechanical-embedding baselines for CDK2, thrombin, p38 and JNK1, and standard single-molecule energy and charge benchmarks were not good predictors of this target-dependent outcome.

Stephen E. Farr, G. de Fabritiis · 0 citations
Preprint Aug 2026

On calculating polar solvation energy of nonrigid proteins in the Poisson-Boltzmann theory

The generalized PB theory is validated using a perturbed two-atom system and a diverse set of proteins with different structures in vacuum and water, demonstrating its accuracy and robustness, regardless of the choice of sharp-interface and diffuse-interface PB models and different numerical solvers.

Matthias Dogbatsey, Yuanzhen Shao, Emil Alexov et al. · 0 citations
Open access Aug 2026

Fast intermolecular interaction energy calculation with the OPLS-AA force field

A fast pipeline based on the OPLS-AA force field is presented that enables the automated calculation of non-bonding intermolecular (dimer) interaction energies derived from a set of small organic (monomer) molecules. To calculate the non-bonding contributions, optimized geometries of the monomer molecules as well as th...

Mirco Daniel, Hannah Kullik, Martin Urban et al. · 0 citations
Jul 2026

Charged Systems in Absolute Binding Free Energy Calculations: An Analytical Electrostatic Approach.

Alchemical free energy perturbation (FEP) is one of the most rigorous methods for predicting protein-ligand binding affinities, yet charged-ligand calculations suffer from finite-size electrostatic artifacts introduced by periodic boundary conditions, which can bias results by several kcal·mol-1. Existing approaches ea...

Runduo Liu, Wanyi Huang, Yufen Yao et al. · 0 citations
Aug 2026

Accurate Atomic Decomposition Method in 3D-RISM Theory via Multi-Input Linear Correction: Application to the Protein Hydrophobic Core.

Solvation free energy (SFE) is a fundamental thermodynamic quantity governing biomolecular processes in solution. Although the atomic decomposition method derived from the Kirkwood charging formula enables site-resolved evaluation of SFE contributions, its application within the three-dimensional reference interaction...

Yutaka Maruyama, Norio Yoshida · 0 citations
Jul 2026

Free Energies of Solvation in Cyclohexane and Water: United-Atom vs All-Atom.

Free energies of solvation (ΔGsol) in a prototypical liquid alkane, cyclohexane, have been computed for 101 organic molecules at 25 °C. Monte Carlo statistical mechanics (MC) was used with free-energy perturbation theory (FEP) and both OPLS united-atom (UA) and all-atom (AA) force fields. Updated OPLS-UA parameters are...

W. Jorgensen, J. Tirado-Rives · 0 citations

We use cookies to run the site and, with your consent, for analytics and to show ads. See our Cookie Policy.