ArticleJournal of chemical information and modeling2019
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
Article in Journal of chemical information and modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Unbiased MD simulations identify lipid binding sites in lipid transfer proteins.The Journal of cell biology · 2024Article
- 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
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- 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
- 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
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics.Frontiers in molecular biosciences · 2022Article
- Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.Angewandte Chemie (International ed. in English) · 2021Article
- Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations.Current research in structural biology · 2021Article
- Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.International journal of molecular sciences · 2020Article
- Protein-ligand binding with the coarse-grained Martini model.Nature communications · 2020Article
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5 authors.
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Abstract
Molecular recognition underpins all specific protein-ligand interactions and is essential for biomolecular functions. The prediction of canonical binding poses and distinguishing binders from nonbinders are much sought after goals. Here, we apply the generalized replica exchange with solute tempering method, gREST, combined with a flat-bottom potential to evaluate binder and nonbinder interactions with a T4 lysozyme Leu99Ala mutant. The buried hydrophobic cavity and possibility of coupled conformational changes in this protein make binding predictions difficult. The present gREST simulations, enabling enhanced flexibilities of the ligand and protein residues near the binding site, sample bindings in multiple poses, and correct portrayal of X-ray structures. The free-energy profiles of binders (benzene, ethylbenzene, and
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