Cargando…

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes

In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for...

Descripción completa

Detalles Bibliográficos
Autores principales:	Jin, Xinsheng, Zhu, Tong, Zhang, John Z. H., He, Xiao
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2018
Materias:	Chemistry
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952040/ https://www.ncbi.nlm.nih.gov/pubmed/29868556 http://dx.doi.org/10.3389/fchem.2018.00150

Ejemplares similares

On the Difference Between Additive and Subtractive QM/MM Calculations
por: Cao, Lili, et al.
Publicado: (2018)

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems
por: Berraud-Pache, Romain, et al.
Publicado: (2018)

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions
por: Mulholland, Adrian J
Publicado: (2007)

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations
por: Voice, Angus T., et al.
Publicado: (2021)

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region
por: Jindal, Garima, et al.
Publicado: (2016)

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase
por: Prejanò, Mario, et al.
Publicado: (2018)

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations
por: Reiter, Sebastian, et al.
Publicado: (2023)

QM/MM Calculations with deMon2k
por: Salahub, Dennis R., et al.
Publicado: (2015)

Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shift Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations
por: Chen, Sijin, et al.
Publicado: (2021)

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase
por: Kulik, Heather J., et al.
Publicado: (2016)

Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code
por: Marcolongo, Juan P., et al.
Publicado: (2018)

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations
por: Korlyukov, Alexander A., et al.
Publicado: (2023)

Resolving the structure of the E(1) state of Mo nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations
por: Van Stappen, Casey, et al.
Publicado: (2019)

An automated framework for NMR chemical shift calculations of small organic molecules
por: Yesiltepe, Yasemin, et al.
Publicado: (2018)

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations
por: Pan, Xiaoliang, et al.
Publicado: (2018)

QM/MM studies on luminescence mechanism of dinuclear copper iodide complexes with thermally activated delayed fluorescence
por: Wang, Qian, et al.
Publicado: (2019)

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings
por: Loco, Daniele, et al.
Publicado: (2019)

Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations
por: Zhen, Yunmei, et al.
Publicado: (2014)

Recent advances in QM/MM free energy calculations using reference potentials()
por: Duarte, Fernanda, et al.
Publicado: (2015)

Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations
por: Torabifard, Hedieh, et al.
Publicado: (2018)

Tuning of dye optical properties by environmental effects: a QM/MM and experimental study
por: Del Frate, Gianluca, et al.
Publicado: (2016)

Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations
por: Liu, Lanxuan, et al.
Publicado: (2019)

DFT Calculations of (31)P NMR Chemical Shifts in Palladium Complexes
por: Kondrashova, Svetlana A., et al.
Publicado: (2022)

Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis
por: Goyal, Puja, et al.
Publicado: (2015)

QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases
por: Escorcia, Andrés M., et al.
Publicado: (2018)

Hybrid QM/MM study of FMO complex with polarized protein-specific charge
por: Jia, Xiangyu, et al.
Publicado: (2015)

MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450(BM3) alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species
por: Dubey, Kshatresh Dutta, et al.
Publicado: (2017)

Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition via Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation
por: Chauhan, Jyoti, et al.
Publicado: (2021)

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes
por: Lence, Emilio, et al.
Publicado: (2018)

The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study
por: Hitzenberger, Manuel, et al.
Publicado: (2017)

Review on the QM/MM Methodologies and Their Application to Metalloproteins
por: Tzeliou, Christina Eleftheria, et al.
Publicado: (2022)

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods
por: Yildiz, Ibrahim, et al.
Publicado: (2018)

MD simulations and QM/MM calculations reveal the key mechanistic elements which are responsible for the efficient C–H amination reaction performed by a bioengineered P450 enzyme
por: Kalita, Surajit, et al.
Publicado: (2021)

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations
por: Sahoo, Sudhir K., et al.
Publicado: (2018)

Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M(pro) by QM/MM computational methods
por: Świderek, Katarzyna, et al.
Publicado: (2020)

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
por: Pérez-Barcia, Álvaro, et al.
Publicado: (2023)

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors
por: Andrikopoulos, Prokopis C., et al.
Publicado: (2021)

Structure–Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations
por: Schulz, Christine E., et al.
Publicado: (2021)

Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study
por: Romero-Téllez, Sonia, et al.
Publicado: (2019)

QM/MM study of the reaction mechanism of sulfite oxidase
por: Caldararu, Octav, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_eife8s2ut5u0ftirmcqk91ci1l