[NMR paper] Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution
Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution
The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with...
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11-13-2023 06:35 PM
[NMR paper] Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Related Articles Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Front Chem. 2018;6:150
Authors: Jin X, Zhu T, Zhang JZH, He X
Abstract
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...
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06-06-2018 01:42 PM
[NMR paper] Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
Related Articles Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
J Chem Theory Comput. 2016 Dec 19;
Authors: Steinmann C, Bratholm LA, Olsen JM, Kongsted J
Abstract
Full-protein NMR shielding constants based on ab initio calculations are desirable since they can assist in...
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12-21-2016 07:20 AM
[NMR paper] AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Related Articles AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
J Biomol NMR. 2015 Aug 2;
Authors: Swails J, Zhu T, He X, Case DA
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects...
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08-04-2015 03:00 PM
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poissonâ??Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation...
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08-02-2015 07:10 AM
Automated Method for Purifying Protein:Ligand Complexes - News-Medical.net
Automated Method for Purifying Protein:Ligand Complexes - News-Medical.net
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Automated Method for Purifying Protein:Ligand Complexes
News-Medical.net
Common techniques for further analyzing protein:ligand complexes to gain structural information include X-ray crystallography, NMR, and cryo-EM. However, a lack of reproducible and robust separation techniques means the purification of protein:ligand ...
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05-20-2015 10:27 AM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Adv Exp Med Biol. 2015;827:49-70
Authors: Zhu T, Zhang JZ, He X
Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
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11-14-2014 08:33 AM
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Michael John, Guido Pintacuda, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting
J. Am. Chem. Soc.; 2006; 128(39) pp 12910 - 12916; (Article)
Abstract:
Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small...
Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes - Frontiers
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