ArticleJournal of computer-aided molecular design2012
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.
Article in Journal of computer-aided molecular design, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 logPhysical chemistry chemical physics : PCCP · 2025Article
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint.Biophysical journal · 2024Article
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- 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
- Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.Physical chemistry chemical physics : PCCP · 2023Article
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
- Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.Journal of computer-aided molecular design · 2022Article
- Thermodynamics of Pillararene•Guest Complexation: Blinded Dataset for the SAMPL9 Challenge.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].Living journal of computational molecular science · 2022Article
- Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge.Journal of computer-aided molecular design · 2021Article
- SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.Journal of computer-aided molecular design · 2021Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
- Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?Journal of computer-aided molecular design · 2021Article
- Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling.International journal of molecular sciences · 2021Article
- Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.The Journal of chemical physics · 2021Article
- Testing automatic methods to predict free binding energy of host-guest complexes in SAMPL7 challenge.Journal of computer-aided molecular design · 2021Article
- AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.Journal of computer-aided molecular design · 2021Article
- SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.Journal of computer-aided molecular design · 2021Article
24 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
The computational prediction of protein-ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands--i.e., host-guest systems--represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challenge for host-guest binding affinities, through the incorporation of 11 new host-guest complexes. Ten participating research groups addressed this challenge with a variety of approaches. Statistical assessment indicates that, although most methods performed well at predicting some general trends in binding affinity, overall accuracy was not high, as all the methods suffered from either poor correlation or high RMS errors or both. There was no clear advantage in using explicit versus implicit solvent models, any particular force field, or any particular approach to conformational sampling. In a few cases, predictions using very similar energy models but different sampling and/or free-energy methods resulted in significantly different results. The protonation states of one host and some guest molecules emerged as key uncertainties beyond the choice of computational approach. The present results have implications for methods development and future blind prediction exercises.
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