ReviewProgress in nuclear magnetic resonance spectroscopy
Chemical shift-based methods in NMR structure determination.
Review in Progress in nuclear magnetic resonance spectroscopy. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts.The journal of physical chemistry. B · 2026Article
- Improving Protein Structure Determination by Integrating Ensemble-Driven Molecular Dynamics with Chemical Shift-Based Restraints.Journal of chemical information and modeling · 2026Article
- Integrating diverse experimental information to assist protein complex structure prediction by GRASP.Nature methods · 2025Article
- Exploring the Frontiers of Computational NMR: Methods, Applications, and Challenges.Chemical reviews · 2025Review
- Solution mapping of MHC-I:TCR interactions using a minimalistic protein system.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs.Biomolecular NMR assignments · 2024Article
- Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition.Nature communications · 2023Article
- NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the MgInternational journal of molecular sciences · 2023Article
- Recent Advances in NMR Protein Structure Prediction with ROSETTA.International journal of molecular sciences · 2023Review
- Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.Peptide science (Hoboken, N.J.) · 2023Article
- Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer).Molecules (Basel, Switzerland) · 2023Article
- Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein.International journal of molecular sciences · 2023Article
- Benchmarking AlphaFold2 on peptide structure prediction.Structure (London, England : 1993) · 2023Article
- Hydrogen Bonding Drives Helical Chirality via 10-Membered Rings in Dipeptide Conjugates of Ferrocene-1,1'-Diamine.International journal of molecular sciences · 2022Article
- Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region.PLoS pathogens · 2022Article
- Structure and Carbohydrate Recognition by the Nonmitogenic Lectin Horcolin.Biochemistry · 2022Article
- Article
- Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.Biophysical journal · 2021Article
- Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift.Frontiers in molecular biosciences · 2021Article
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Authors and funding
3 authors.
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Abstract
Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools.
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