Cargando…

Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC...

Descripción completa

Detalles Bibliográficos
Autores principales:	Duan, Li L., Feng, Guo Q., Zhang, Qing G.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2016
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4979035/ https://www.ncbi.nlm.nih.gov/pubmed/27507430 http://dx.doi.org/10.1038/srep31488

Ejemplares similares

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations
por: Duan, Li L., et al.
Publicado: (2017)

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model
por: Zeng, Xiaojun, et al.
Publicado: (2016)

Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase
por: Zhang, Ji-Long, et al.
Publicado: (2012)

Structure and Behavior of Human α-Thrombin upon Ligand Recognition: Thermodynamic and Molecular Dynamics Studies
por: Silva, Vivian de Almeira, et al.
Publicado: (2011)

Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands
por: Troisi, Romualdo, et al.
Publicado: (2021)

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations
por: Chen, Jianzhong, et al.
Publicado: (2019)

Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation
por: Fukunishi, Yoshifumi, et al.
Publicado: (2012)

The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model
por: Guo, Yue, et al.
Publicado: (2019)

Insights into Ligand Binding to PreQ(1) Riboswitch Aptamer from Molecular Dynamics Simulations
por: Gong, Zhou, et al.
Publicado: (2014)

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
por: Reif, Maria M, et al.
Publicado: (2014)

Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations
por: Sakkiah, Sugunadevi, et al.
Publicado: (2018)

Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein
por: Long, Dong, et al.
Publicado: (2009)

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design
por: Tan, Yaw Sing, et al.
Publicado: (2016)

The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations
por: Lai, Hien T. T., et al.
Publicado: (2021)

Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility
por: Wallraven, Kerstin, et al.
Publicado: (2020)

Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations
por: Kienlein, Maximilian, et al.
Publicado: (2020)

Thrombin-Binding Aptamer with Inversion of Polarity Sites (IPS): Effect on DNAzyme Activity and Anticoagulant Properties
por: Kosman, Joanna, et al.
Publicado: (2021)

Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations
por: Li, Haiyan, et al.
Publicado: (2021)

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations
por: Ono, Junichi, et al.
Publicado: (2022)

Study of Materials Deformation in Nanometric Cutting by Large-scale Molecular Dynamics Simulations
por: Pei, QX, et al.
Publicado: (2009)

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations
por: Sultan, Mohammad M., et al.
Publicado: (2014)

Molecular simulations of SSTR2 dynamics and interaction with ligands
por: Gervasoni, Silvia, et al.
Publicado: (2023)

A new modified thrombin binding aptamer containing a 5′–5′ inversion of polarity site
por: Martino, Luigi, et al.
Publicado: (2006)

Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein
por: Fu, Yi, et al.
Publicado: (2018)

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale
por: Khazanov, Nickolay A., et al.
Publicado: (2013)

Preliminary Molecular Dynamic Simulations of the Estrogen Receptor Alpha Ligand Binding Domain from Antagonist to Apo
por: McGee, T. Dwight, et al.
Publicado: (2008)

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
por: Dolenc, Jožica, et al.
Publicado: (2005)

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks
por: Rudling, Axel, et al.
Publicado: (2018)

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations
por: Jenwitheesuk, Ekachai, et al.
Publicado: (2003)

Editorial: Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics
por: Chu, Xiakun, et al.
Publicado: (2021)

Semi-automated thrombin dynamics applying the ST Genesia thrombin generation assay
por: Carlo, Audrey, et al.
Publicado: (2022)

Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods
por: Wang, Debby D., et al.
Publicado: (2020)

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols
por: Bhati, Agastya P., et al.
Publicado: (2022)

Changes in Protonation States of In-Pathway Residues can Alter Ligand Binding Pathways Obtained From Spontaneous Binding Molecular Dynamics Simulations
por: Girame, Helena, et al.
Publicado: (2022)

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins
por: Kapoor, Karan, et al.
Publicado: (2022)

Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations
por: Lamprakis, Christos, et al.
Publicado: (2015)

Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations
por: Carli, Matteo, et al.
Publicado: (2020)

Dynamic allostery in thrombin—a review
por: Komives, Elizabeth A.
Publicado: (2023)

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
por: Tan, Cheng, et al.
Publicado: (2022)

Towards the simulation of large scale protein–ligand interactions on NISQ-era quantum computers
por: Malone, Fionn D., et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_1s19sr9so8ir2stot0kqkosd88