Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately...
[NMR paper] Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion.
Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion.
Related Articles Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion.
J Phys Chem B. 2020 Jun 05;:
Authors: Marcellini M, Nguyen MH, Martin M, Hologne M, Walker O
Abstract
Among the various biophysical methods available to investigate protein dynamics, NMR present the ability to scrutinize...
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06-06-2020 04:36 PM
[NMR paper] 13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.
13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.
Related Articles 13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.
J Chem Theory Comput. 2020 Apr 08;:
Authors: Anderson JS, Hernandez G, LeMaster DM
Abstract
Molecular simulations with seven current AMBER- and CHARMM-based force fields yield markedly differing internal bond vector autocorrelation function...
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04-09-2020 07:27 PM
[NMR paper] Evaluating Amber force fields using computed NMR chemical shifts.
Evaluating Amber force fields using computed NMR chemical shifts.
Related Articles Evaluating Amber force fields using computed NMR chemical shifts.
Proteins. 2017 Jul 08;:
Authors: Koes DR, Vries JK
Abstract
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations....
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07-09-2017 11:44 PM
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters
Abstract
Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari–Szabo squared generalized order parameter (O2)...
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04-04-2016 12:40 PM
[NMR paper] On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters.
Protein Sci. 2016 Mar 14;
Authors: O'Brien ES, Wand AJ, Sharp KA
Abstract
Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify molecular dynamics force fields, most...
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03-19-2016 09:23 PM
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters
On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters
Abstract
Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify molecular dynamics force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or NMR chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O2) values of...
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03-15-2016 11:57 AM
[NMR paper] CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
J Comput Chem. 2013 Jul 6;
Authors: Huang J, Mackerell AD
Abstract
Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR...
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07-09-2013 02:47 PM
[NMR paper] Generation of native-like protein structures from limited NMR data, modern force fiel
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
Related Articles Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
J Biomol NMR. 2005 Jan;31(1):59-64
Authors: Chen J, Won HS, Im W, Dyson HJ, Brooks CL
Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality...
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data
Linear Mode
