ArticleJournal of computational chemistry2013
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.
Article in Journal of computational chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 64 citations in OpenAlex.
- HalogenatedRSC advances · 2025Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
- Interplay of structure and photophysics of individualized rod-shaped graphene quantum dots with up to 132 sp² carbon atoms.Nature communications · 2023Article
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
- Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.Scientific reports · 2022Article
- Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities.ACS catalysis · 2022Review
- Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.Nature protocols · 2022Review
- Molecular Modeling of ABHD5 Structure and Ligand Recognition.Frontiers in molecular biosciences · 2022Article
- Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [MJournal of chemical information and modeling · 2021Article
- Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.Journal of chemical theory and computation · 2020Article
- Ligand binding free-energy calculations with funnel metadynamics.Nature protocols · 2020Article
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.Journal of computer-aided molecular design · 2020Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
- Best Practices for Alchemical Free Energy Calculations [Article v1.0].Living journal of computational molecular science · 2020Article
- Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.Journal of chemical theory and computation · 2019Article
- Using AMBER18 for Relative Free Energy Calculations.Journal of chemical information and modeling · 2019Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.Journal of chemical theory and computation · 2018Article
- Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.Physical chemistry chemical physics : PCCP · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
This article addresses calculations of the standard free energy of binding from molecular simulations in which a bound ligand is extracted from its binding site by steered molecular dynamics (MD) simulations or equilibrium umbrella sampling (US). Host-guest systems are used as test beds to examine the requirements for obtaining the reversible work of ligand extraction. We find that, for both steered MD and US, marked irreversibilities can occur when the guest molecule crosses an energy barrier and suddenly jumps to a new position, causing dissipation of energy stored in the stretched molecule(s). For flexible molecules, this occurs even when a stiff pulling spring is used, and it is difficult to suppress in calculations where the spring is attached to the molecules by single, fixed attachment points. We, therefore, introduce and test a method, fluctuation-guided pulling, which adaptively adjusts the spring's attachment points based on the guest's atomic fluctuations relative to the host. This adaptive approach is found to substantially improve the reversibility of both steered MD and US calculations for the present systems. The results are then used to estimate standard binding free energies within a comprehensive framework, termed attach-pull-release, which recognizes that the standard free energy of binding must include not only the pulling work itself, but also the work of attaching and then releasing the spring, where the release work includes an accounting of the standard concentration to which the ligand is discharged.
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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.