ArticleJournal of chemical theory and computation2019
Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Phosphatidylinositol transfer protein α binds microcolins in its open conformation.Acta crystallographica. Section D, Structural biology · 2026Article
- Machine Learning in Enhancing Protein Binding Sites Predictions - What Has Changed Since Then?Combinatorial chemistry & high throughput screening · 2025Review
- Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions.The journal of physical chemistry. B · 2024Article
- CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.Journal of chemical information and modeling · 2023Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- Mining for Ligandable Cavities in RNA.ACS medicinal chemistry letters · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.Journal of chemical information and modeling · 2021Article
- Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR).International journal of biological macromolecules · 2020Review
- Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.Journal of chemical information and modeling · 2020Article
- Exploring the computational methods for protein-ligand binding site prediction.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate modeling of ligand-binding-site structures plays a critical role in structure-based virtual screening. However, the structures of the ligand-binding site in most predicted protein models are generally of low quality and need refinements. In this work, we present a ligand-binding-site structure refinement protocol using molecular dynamics simulation with restraints derived from predicted binding site templates. Our benchmark validation shows great performance for 40 diverse sets of proteins from the Astex list. The ligand-binding sites on modeled protein structures are consistently refined using our method with an average Cα RMSD improvement of 0.90 Å. Comparison of ligand binding modes from ligand docking to initial unrefined and refined structures shows an average of 1.97 Å RMSD improvement in the refined structures. These results demonstrate a promising new method of structure refinement for protein ligand-binding-site structures.
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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.