ArticleJournal of biomolecular NMR2007
Predicting 13Calpha chemical shifts for validation of protein structures.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- Assessing the One-Bond CThe journal of physical chemistry. B · 2020Article
- Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2.Scientific reports · 2019Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.Nucleic acids research · 2014Article
- acACS: improving the prediction accuracy of protein subcellular locations and protein classification by incorporating the average chemical shifts composition.TheScientificWorldJournal · 2014Article
- Probing slowly exchanging protein systems via ¹³Cα-CEST: monitoring folding of the Im7 protein.Journal of biomolecular NMR · 2013Article
- Improved chemical shift prediction by Rosetta conformational sampling.Journal of biomolecular NMR · 2012Article
- Identification of helix capping and b-turn motifs from NMR chemical shifts.Journal of biomolecular NMR · 2012Article
- Chemical shift tensors: theory and application to molecular structural problems.Progress in nuclear magnetic resonance spectroscopy · 2011Review
- Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.Journal of biomolecular NMR · 2010Article
- Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach.Journal of biomolecular NMR · 2010Article
- Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.Accounts of chemical research · 2009Article
- Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.Journal of biomolecular NMR · 2009Article
- What can we learn by computing 13Calpha chemical shifts for X-ray protein models?Acta crystallographica. Section D, Biological crystallography · 2009Article
- Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution.Journal of computational chemistry · 2009Article
- Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures.Proteins · 2008Article
- Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed (13)C(alpha) chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree-Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMR-derived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed (13)C(alpha) chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed (13)C(alpha) chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.
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