ArticleJournal of chemical theory and computation2023
AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.
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 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Molecular characterisation of the trafficking rescue of defective ABCB4 variants by roscovitine analogues.Scientific reports · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.The journal of physical chemistry. B · 2025Article
- DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation.Journal of chemical theory and computation · 2025Article
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- ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation.Journal of chemical theory and computation · 2025Article
- Development of a Second-Generation,Journal of medicinal chemistry · 2025Article
- Discovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach.Acta pharmaceutica Sinica. B · 2024Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.Journal of chemical information and modeling · 2024Article
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.The journal of physical chemistry. B · 2024Article
- Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.Journal of chemical information and modeling · 2024Article
- Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators.Journal of chemical information and modeling · 2024Article
- Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.The journal of physical chemistry. B · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
We develop a framework for the design of optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for so-called "softcore" potentials. We describe the implementation and testing of this framework in the GPU-accelerated AMBER software suite. The new optimized alchemical transformation pathways integrate a number of important features, including (1) the use of smoothstep functions to stabilize behavior near the transformation end points, (2) consistent power scaling of Coulomb and Lennard-Jones (LJ) interactions with unitless control parameters to maintain balance of electrostatic attractions and exchange repulsions, (3) pairwise form based on the LJ contact radius for the effective interaction distance with separation-shifted scaling, and (4) rigorous smoothing of the potential at the nonbonded cutoff boundary. The new softcore potential form is combined with smoothly transforming nonlinear λ weights for mixing specific potential energy terms, along with flexible λ-scheduling features, to enable robust and stable alchemical transformation pathways. The resulting pathways are demonstrated and tested, and shown to be superior to the traditional methods in terms of numerical stability and minimal variance of the free energy estimates for all cases considered. The framework presented here can be used to design new alchemical enhanced sampling methods, and leveraged in robust free energy workflows for large ligand data sets.
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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.