ArticleThe journal of physical chemistry. B2017
Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 74 citations in OpenAlex.
- Determination of coverage-dependent surface reaction rates using λ-dynamics: Application to molecular desorption.The journal of physical chemistry. C, Nanomaterials and interfaces · 2026Article
- Accelerated Combinatorial Drug Design for Human Immunodeficiency Virus Resistance through Seeded Multisite λ-Dynamics.Journal of chemical theory and computation · 2026Article
- Sampling the Grand Canonical Ensemble with Multisite λ Dynamics.The journal of physical chemistry letters · 2026Article
- EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery.bioRxiv : the preprint server for biology · 2026Article
- SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.The journal of physical chemistry. B · 2025Article
- 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
- Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics.Journal of chemical information and modeling · 2025Article
- Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations.The journal of physical chemistry letters · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Predicting Thermodynamic Stability at Protein G Sites with Deleterious Mutations Using λ-Dynamics with Competitive Screening.The journal of physical chemistry letters · 2025Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- How to Sample Dozens of Substitutions per Site with λ Dynamics.Journal of chemical theory and computation · 2024Article
- A λ-Dynamics Investigation of InsulinJournal of chemical information and modeling · 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
- A λ-dynamics investigation of insulinbioRxiv : the preprint server for biology · 2024Article
- Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Multisite λ dynamics (MSλD) is a powerful emerging method in free energy calculation that allows prediction of relative free energies for a large set of compounds from very few simulations. Calculating free energy differences between substituents that constitute large volume or flexibility jumps in chemical space is difficult for free energy methods in general, and for MSλD in particular, due to large free energy barriers in alchemical space. This study demonstrates that a simple biasing potential can flatten these barriers and introduces an algorithm that determines system specific biasing potential coefficients. Two sources of error, deep traps at the end points and solvent disruption by hard-core potentials, are identified. Both scale with the size of the perturbed substituent and are removed by sharp biasing potentials and a new soft-core implementation, respectively. MSλD with landscape flattening is demonstrated on two sets of molecules: derivatives of the heat shock protein 90 inhibitor geldanamycin and derivatives of benzoquinone. In the benzoquinone system, landscape flattening leads to 2 orders of magnitude improvement in transition rates between substituents and robust solvation free energies. Landscape flattening opens up new applications for MSλD by enabling larger chemical perturbations to be sampled with improved precision and accuracy.
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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.