ArticleJournal of biomolecular NMR2015
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- NMR crystallography reveals active-site protonation states of Toho-1 β-lactamase in complex with avibactam.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Application of NMR to Large RNAs.Journal of molecular biology · 2025Review
- Selective [9-Chembiochem : a European journal of chemical biology · 2025Article
- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- Probing Protein-Ligand Methyl-π Interaction Geometries through Chemical Shift Measurements of Selectively Labeled Methyl Groups.Journal of medicinal chemistry · 2024Article
- Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics.The journal of physical chemistry letters · 2024Review
- Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins.Science advances · 2024Article
- Multitasking Pharmacophores Support Cabotegravir-Based Long-Acting HIV Pre-Exposure Prophylaxis (PrEP).Molecules (Basel, Switzerland) · 2024Article
- An RNA excited conformational state at atomic resolution.Nature communications · 2023Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Dynamic Coupling of Tyrosine 185 with the Bacteriorhodopsin Photocycle, as Revealed by Chemical Shifts, Assisted AF-QM/MM Calculations and Molecular Dynamic Simulations.International journal of molecular sciences · 2021Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- A quantitative model predicts how mNature communications · 2021Article
- Structural and Molecular Dynamics ofACS infectious diseases · 2021Article
- Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE iminoMagnetic resonance (Gottingen, Germany) · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
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4 authors.
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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 Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.
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