ArticleThe journal of physical chemistry. B2024
Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Sampling the Grand Canonical Ensemble with Multisite λ Dynamics.The journal of physical chemistry letters · 2026Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.Journal of chemical theory and computation · 2025Article
- Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations.The journal of physical chemistry letters · 2025Article
- Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations.The journal of physical chemistry. B · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
Alchemical free energy (AFE) calculations can predict binding affinity changes as a function of structural modifications and have become powerful tools for lead optimization and drug discovery. Central to the setup and performance of AFE calculations is the manner of mapping alchemical transformations, known as the topology model. Single, dual, and hybrid topology models have been used with various AFE methods in the field. In recent works, λ-dynamics (λD) free energy calculations, specifically, have preferred the use of a hybrid multiple topology (HMT) for sampling multiple ligand perturbations. In this work, we evaluate a new topology method called ligand overlay (LO) for use with λD-based calculations, including the recently introduced λ-dynamics with a bias-updated Gibbs sampling (LaDyBUGS) approach. LO is a full multiple topology model that allows entire ligands to be sampled and restrained within a λ-dynamics framework. Relative binding free energies were computed with HMT or LO topology models with LaDyBUGS for 45 ligands across five protein benchmark systems. An overall Pearson
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Registered trials
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