ArticleJournal of biomolecular NMR2003
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.
Article in Journal of biomolecular NMR, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 241 papers.
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241 citing papers in PubMed.
- Energy Landscape Analysis of Membrane Proteins Using NMR-Based Hybrid Restraint Potentials.Journal of chemical theory and computation · 2026Article
- Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts.The journal of physical chemistry. B · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
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- Solid-state NMR of membrane peptides and proteins in the lipid cubic phase.Biophysical journal · 2025Article
- Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin.The Biochemical journal · 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
- EFG-CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models.Protein science : a publication of the Protein Society · 2024Article
- Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin.Journal of chemical information and modeling · 2024Article
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
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- Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering.The journal of physical chemistry. B · 2023Article
- Atomic-level structure determination of amorphous molecular solids by NMR.Nature communications · 2023Article
- The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs.RSC advances · 2023Review
- Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data.Journal of chemical theory and computation · 2022Article
- Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97.Communications chemistry · 2022Article
- A glutamine-based single α-helix scaffold to target globular proteins.Nature communications · 2022Article
- High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations.International journal of molecular sciences · 2022Article
- α-Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
181 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http://redpoll.pharmacy.ualberta.ca.
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