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dc.contributor.author
Vila Jorge A.  
dc.contributor.author
Arnautova, Yelena A.  
dc.contributor.author
Martín, Osvaldo Antonio  
dc.contributor.author
Scheraga, Harold A.  
dc.date.available
2024-05-15T12:24:09Z  
dc.date.issued
2009-09  
dc.identifier.citation
Vila Jorge A.; Arnautova, Yelena A.; Martín, Osvaldo Antonio; Scheraga, Harold A.; Quantum-mechanics-derived 13Cα chemical shift server ( CheShift) for protein structure validation; National Academy of Sciences; Proceedings of the National Academy of Sciences of The United States of America; 106; 40; 9-2009; 16972-16977  
dc.identifier.issn
0027-8424  
dc.identifier.uri
http://hdl.handle.net/11336/235402  
dc.description.abstract
A server (CheShift) has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα 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 13Cα chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13Cα 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 Å. 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 13Cα chemical shifts are available. CheShift is available as a web server.  
dc.format
application/pdf  
dc.language.iso
eng  
dc.publisher
National Academy of Sciences  
dc.rights
info:eu-repo/semantics/openAccess  
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/  
dc.subject
CHEMICAL SHIFT PREDICTION  
dc.subject
DFT CALCULATIONS  
dc.subject
VALIDATION SERVER  
dc.subject.classification
Biofísica  
dc.subject.classification
Ciencias Biológicas  
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS  
dc.title
Quantum-mechanics-derived 13Cα chemical shift server ( CheShift) for protein structure validation  
dc.type
info:eu-repo/semantics/article  
dc.type
info:ar-repo/semantics/artículo  
dc.type
info:eu-repo/semantics/publishedVersion  
dc.date.updated
2024-05-03T13:59:00Z  
dc.journal.volume
106  
dc.journal.number
40  
dc.journal.pagination
16972-16977  
dc.journal.pais
Estados Unidos  
dc.journal.ciudad
Washington DC  
dc.description.fil
Fil: Vila Jorge A.. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina  
dc.description.fil
Fil: Arnautova, Yelena A.. Cornell University; Estados Unidos  
dc.description.fil
Fil: Martín, Osvaldo Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina  
dc.description.fil
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos  
dc.journal.title
Proceedings of the National Academy of Sciences of The United States of America  
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://www.pnas.org/content/106/40/16972.long  
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://www.pnas.org/doi/full/10.1073/pnas.0908833106  
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1073/pnas.0908833106