ArticleChemical science2017
Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics.
Article in Chemical science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
21 citing papers in PubMed.
- Microscopic Insights into a Ligand Escape Pathway and Energetics in Leucine-Isoleucine-Valine Binding Protein.ACS omega · 2026Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Structural basis for substrate and inhibitor recognition of human multidrug transporter MRP4.Communications biology · 2023Article
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Structural Analysis and Conformational Dynamics of Short Helical Hyperphosphorylated Segments of Tau Protein (Sequence 254-290) in Alzheimer's Disease: A Molecular Dynamics Simulation Study.Frontiers in molecular biosciences · 2022Article
- Best practices for time-resolved serial synchrotron crystallography.Acta crystallographica. Section D, Structural biology · 2022Review
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Temperature artifacts in protein structures bias ligand-binding predictions.Chemical science · 2021Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 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
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Protein-ligand binding with the coarse-grained Martini model.Nature communications · 2020Article
- Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design.Journal of chemical theory and computation · 2020Article
- Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness.Biophysical journal · 2019Article
- Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics.Nature communications · 2019Article
- Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.Journal of chemical information and modeling · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The behaviour of biomolecular systems is governed by their thermodynamic and kinetic properties. It is thus important to be able to calculate, for example, both the affinity and rate of binding and dissociation of a protein-ligand complex, or the populations and exchange rates between distinct conformational states. Because these are typically rare events, calculating these properties from long molecular dynamics simulations remains extremely difficult. Instead, one often adopts a divide-and-conquer strategy in which equilibrium free-energy differences and the fastest state-to-state transition (
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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.