ArticleNature communications2021
The role of water in host-guest interaction.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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Who cites it
33 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Targeting the intrinsically disordered AR-NTD through a machine learning-based enhanced sampling workflow.Nature communications · 2026Article
- Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables.Journal of computer-aided molecular design · 2026Article
- A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies.The journal of physical chemistry letters · 2026Article
- Committors without Descriptors.Journal of chemical theory and computation · 2026Article
- Decoding Allosteric Inhibition in MALT1: The Hidden Role of Conformational Plasticity in Metastable States via Biased MD and Deep Learning.The journal of physical chemistry. B · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Data-driven enhanced sampling of mechanistic pathways.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Dynamics and Interplay of the Binding Pockets in the Glycine Receptor.Journal of chemical information and modeling · 2025Article
- Improved Free-Energy Estimates for the Permeation of Bulky Antibiotic Molecules through Porin Channels Using Temperature-Accelerated Sliced Sampling.Journal of chemical theory and computation · 2025Article
- Machine Learning in Enhancing Protein Binding Sites Predictions - What Has Changed Since Then?Combinatorial chemistry & high throughput screening · 2025Review
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.Journal of chemical information and modeling · 2024Article
- Absolute Binding Free Energies with OneOPES.The journal of physical chemistry letters · 2024Article
- Enhanced Sampling with Machine Learning.Annual review of physical chemistry · 2024Review
- Dynamic Chemistry Toolbox for Advanced Sustainable Materials.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Effective data-driven collective variables for free energy calculations from metadynamics of paths.PNAS nexus · 2024Article
- Cation Chloride Cotransporter NKCC1 Operates through a Rocking-Bundle Mechanism.Journal of the American Chemical Society · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the main applications of atomistic computer simulations is the calculation of ligand binding free energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling is an obstacle in simulations due to the frequent appearance of kinetic bottlenecks in the free energy landscape. Very often this difficulty is circumvented by enhanced sampling techniques. Typically, these techniques depend on the introduction of appropriate collective variables that are meant to capture the system's degrees of freedom. In ligand binding, water has long been known to play a key role, but its complex behaviour has proven difficult to fully capture. In this paper we combine machine learning with physical intuition to build a non-local and highly efficient water-describing collective variable. We use it to study a set of host-guest systems from the SAMPL5 challenge. We obtain highly accurate binding free energies and good agreement with experiments. The role of water during the binding process is then analysed in some detail.
Identifiers
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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.