ArticleProceedings of the National Academy of Sciences of the United States of America2009
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Predicting chemical shifts with graph neural networks.Chemical science · 2021Article
- Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.Biophysical journal · 2019Article
- Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.Biophysical journal · 2019Article
- Chemical shifts in molecular solids by machine learning.Nature communications · 2018Article
- Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.Frontiers in chemistry · 2018Article
- Article
- Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin.The journal of physical chemistry. B · 2017Article
- Protein structure refinement using a quantum mechanics-based chemical shielding predictor.Chemical science · 2017Article
- Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.Computational & theoretical chemistry · 2017Article
- Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Article
- Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.Nucleic acids research · 2014Article
- Factors affecting the computation of the 13C shielding in disaccharides.Journal of computational chemistry · 2014Article
- An overview of tools for the validation of protein NMR structures.Journal of biomolecular NMR · 2014Review
- Are accurate computations of the 13C' shielding feasible at the DFT level of theory?Journal of computational chemistry · 2014Article
- FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.PeerJ · 2014Article
- Physics-based method to validate and repair flaws in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.Journal of biomolecular NMR · 2013Article
- Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.Proteins · 2013Article
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4 authors.
Funding
Abstract
A server (CheShift) has been developed to predict (13)C(alpha) chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the phi, psi, omega, chi1 and chi2 torsional angles for all 20 naturally occurring amino acids. Their (13)C(alpha) chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted (13)C(alpha) chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 A or better resolution, for which sets of (13)C(alpha) chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 A. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed (13)C(alpha) chemical shifts are available. CheShift is available as a web server.
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