ArticleProceedings of the National Academy of Sciences of the United States of America2012
Sampling protein motion and solvent effect during ligand binding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
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- From Apo to Ligand-Bound: Unraveling PPARγ-LBD Conformational Shifts via Advanced Molecular Dynamics.ACS omega · 2025Article
- Unsupervised learning of collective variables for conformational sampling of cyclic peptides.Methods in enzymology · 2025Article
- Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine AChem · 2024Article
- Regulation of microtubule dynamics and function in living cellsChemical science · 2024Article
- Zirconium Coordination Chemistry and Its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics.ACS omega · 2023Article
- OneOPES, a Combined Enhanced Sampling Method to Rule Them All.Journal of chemical theory and computation · 2023Article
- Cell-free Biosynthesis of Peptidomimetics.Biotechnology and bioprocess engineering : BBE · 2023Review
- Water regulates the residence time of Benzamidine in Trypsin.Nature communications · 2022Article
- Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.Frontiers in bioinformatics · 2022Article
- Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands.Frontiers in endocrinology · 2022Review
- Computational Tools for Accurate Binding Free-Energy Prediction.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein.Molecules (Basel, Switzerland) · 2021Review
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process.Journal of chemical theory and computation · 2021Article
- The role of water in host-guest interaction.Nature communications · 2021Article
- Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels.RSC advances · 2020Article
- A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors.The Journal of chemical physics · 2020Article
- Ligand binding free-energy calculations with funnel metadynamics.Nature protocols · 2020Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
An exhaustive description of the molecular recognition mechanism between a ligand and its biological target is of great value because it provides the opportunity for an exogenous control of the related process. Very often this aim can be pursued using high resolution structures of the complex in combination with inexpensive computational protocols such as docking algorithms. Unfortunately, in many other cases a number of factors, like protein flexibility or solvent effects, increase the degree of complexity of ligand/protein interaction and these standard techniques are no longer sufficient to describe the binding event. We have experienced and tested these limits in the present study in which we have developed and revealed the mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase. We have first performed a large number of docking calculations, which unfortunately failed to yield reliable results due to the dynamical character of the enzyme and the complex role of the solvent. Thus, we have stepped up the computational strategy using a protocol based on metadynamics. Our approach has allowed dealing with protein motion and solvation during ligand binding and finally identifying the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one.
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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.