ArticleJournal of biomolecular NMR2007
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology.
Article in Journal of biomolecular NMR, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers.
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Who cites it
154 citing papers in PubMed.
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- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering.Journal of chemical information and modeling · 2024Article
- Quantitative Characterization of Chain-Flipping of Acyl Carrier Protein ofJournal of the American Chemical Society · 2024Article
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- Hfq C-terminal region forms a β-rich amyloid-like motif without perturbing the N-terminal Sm-like structure.Communications biology · 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
- Backbone Torsion Angle Determination Using Proton Detected Magic-Angle Spinning Nuclear Magnetic Resonance.The journal of physical chemistry letters · 2022Article
- Structural Changes of β-Casein Induced by Temperature and pH Analysed by Nuclear Magnetic Resonance, Fourier-Transform Infrared Spectroscopy, and Chemometrics.Molecules (Basel, Switzerland) · 2021Article
- Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS.Journal of the American Chemical Society · 2021Article
- Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.Nucleic acids research · 2021Article
- Merging NMR Data and Computation Facilitates Data-Centered Research.Frontiers in molecular biosciences · 2021Review
- Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy.Frontiers in molecular biosciences · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1.Biophysical journal · 2020Article
- Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.PLoS computational biology · 2020Article
94 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in phi/psi/chi(1 )torsion angles and sequence similarity to the query triplet of interest. The database contains (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C' chemical shifts for 200 proteins for which a high resolution X-ray (< or =2.4 A) structure is available. The relative importance of the weighting factors for the phi/psi/chi(1) angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C', respectively, including outliers.
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