ArticleJournal of computer-aided molecular design2022
An overview of the SAMPL8 host-guest binding challenge.
Article in Journal of computer-aided molecular design, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Mapping the avoid-ome: a systematic open-science approach to predictive ADMET.Nature communications · 2026Review
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data.Journal of chemical information and modeling · 2026Article
- LamNet: an alchemical-path-aware graph neural network to accelerate binding free energy calculations for drug discovery and beyond.National science review · 2026Article
- Quantum mechanics in drug design: Progress, challenges, and future frontiers.Communicative & integrative biology · 2026Review
- Article
- CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.Journal of chemical information and modeling · 2025Article
- Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 logPhysical chemistry chemical physics : PCCP · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- Partially Sulfated Pillar[5]Arenes: Synthesis and Molecular Recognition Properties.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.The Journal of chemical physics · 2025Article
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations.The journal of physical chemistry. B · 2024Article
- Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations.Physical chemistry chemical physics : PCCP · 2024Article
- Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals.The Journal of chemical physics · 2024Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins.Physical chemistry chemical physics : PCCP · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
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4 authors.
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Abstract
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host-guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host-guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach (ATM/GAFF2-AM1BCC/TIP3P/HREM) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons; for example, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group sampling and/or guest starting pose, providing guidance to help improve future studies on these systems.
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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 Socratic graph.