ArticleJournal of computer-aided molecular design2021
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.
Article in Journal of computer-aided molecular design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation.Journal of chemical theory and computation · 2026Article
- Achieving Chemical Accuracy in Cyclodextrin Host-Guest Binding via Integrative Atomistic Modelling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Ligand-Binding Free Energy Simulations of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.Nature communications · 2023Article
- Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.Physical chemistry chemical physics : PCCP · 2023Article
- Host Dynamics under General-Purpose Force Fields.Molecules (Basel, Switzerland) · 2023Article
- Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation.Molecules (Basel, Switzerland) · 2023Article
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
- Evaluating the use of absolute binding free energy in the fragment optimisation process.Communications chemistry · 2022Article
- Alchemical absolute protein-ligand binding free energies for drug design.Chemical science · 2021Article
- Assigning confidence to molecular property prediction.Expert opinion on drug discovery · 2021Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
- Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.Communications chemistry · 2021Article
- Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.The journal of physical chemistry. B · 2021Article
- Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone-Wales Defects as Drug Carriers: A Molecular Dynamics Approach.Molecules (Basel, Switzerland) · 2021Article
- SAMPL7 blind predictions using nonequilibrium alchemical approaches.Journal of computer-aided molecular design · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.Journal of computer-aided molecular design · 2021Article
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4 authors.
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Abstract
In the current work we report on our participation in the SAMPL7 challenge calculating absolute free energies of the host-guest systems, where 2 guest molecules were probed against 9 hosts-cyclodextrin and its derivatives. Our submission was based on the non-equilibrium free energy calculation protocol utilizing an averaged consensus result from two force fields (GAFF and CGenFF). The submitted prediction achieved accuracy of [Formula: see text] in terms of the unsigned error averaged over the whole dataset. Subsequently, we further report on the underlying reasons for discrepancies between our calculations and another submission to the SAMPL7 challenge which employed a similar methodology, but disparate ligand and water force fields. As a result we have uncovered a number of issues in the dihedral parameter definition of the GAFF 2 force field. In addition, we identified particular cases in the molecular topologies where different software packages had a different interpretation of the same force field. This latter observation might be of particular relevance for systematic comparisons of molecular simulation software packages. The aforementioned factors have an influence on the final free energy estimates and need to be considered when performing alchemical calculations.
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