The services provided by this server are free of charge only for Academic use. If you find CheShift-2 useful for your own research please cite us using, at least, reference 1.
Acknowledgement
We want to thanks to Angel Herráez for the code behind the "Save Snapshot" button and for the code to dynamically size the Jsmol applet.
We also want to thanks Robert Hanson (and other developers) for making Jsmol possible. JSmol is a Java-free version of the Jmol applet using only HTML5.
A brief description of the method
CheShift has been developed to predict 13Cα and 13Cβ chemical shifts of protein structures. It is based on the generation of ~1,200,000 conformations as a function of the torsional angles for all 20 naturally occurring amino acids. Their 13Cα and 13Cβ chemical shifts were computed at the DFT level. For further details on the CheShift 13Cα chemical shift predictions please read reference 5. The description of the visual, per residue validation, was discused in reference 2. Other references related to the method and its applications are listed below.
References
1.- Martin O.A. Arnautova Y.A. Icazatti A.A. Scheraga H.A. and Vila J.A. A Physics-Based Method to Validate and Repair Flaws in Protein Structures. Proc Natl Acad Sci USA 2013. 110, 16826-16831.
2.- Martin O.A. Vila J.A. and Scheraga H.A. CheShift-2: Graphic validation of protein structures. Bioinformatics 2012. 28(11), 1538-1539.
3.- Vila, J. A., Serrano, P., Wüthrich, K., & Scheraga, H. A. Sequential nearest-neighbor effects on computed (13)C (alpha) chemical shifts. J Biomol NMR 2010, 48(1), 23-30.
4.- Martin, O. A., Villegas, M. E., Vila, J. A., & Scheraga, H. A. (2010). Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach. J Biomol NMR 2010, 46(3), 217-25.
5.- Vila J.A., Arnautova Y.A., Martin O.A. and Scheraga H.A. Quantum-Mechanics-Derived 13Cα Chemical Shift Server (CheShift) for Protein Structure Validation. Proc Natl Acad Sci USA 2009, 106(40), 16972-16977.
6.- Vila J.A. and Scheraga H.A. Assessing the Accuracy of Protein Structures by Quantum Mechanical Computations of 13Cα Chemical Shifts. Acc Chem Res 2009, 42(10) 1545-53..
7.- Villegas M.E.; Vila J.A.; Scheraga H.A. Effects of Side-Chain Orientation on the 13C Chemical Shifts of Antiparallel β-sheet Model Peptides. J Biomol NMR 2007, 37, 137-146.
8.- Vila J.A.; Villegas M.E.; Baldoni H.A.; Scheraga H.A. Predicting 13Cα chemical shifts for validation of protein structures. J Biomol NMR 2007, 38, 221-235.
9.- Vila J.A.; Arnautova Y.A.; Scheraga H.A. Use of 13Cα chemical shifts for accurate determination of β-Sheet structures in solution. Proc Natl Acad Sci USA 2008, 105, 1891-1896.
10.- Vila, J. A.; Aramini J. M.; Rossi P.; Kuzin A.; Su M.; Seetharaman J.; Xiao R.; Tong L.; Montelione G. T.; H. A. Scheraga. Quantum Chemical 13C Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation. Proc Natl Acad Sci USA 2008, 38, 14389-14394.
11.- Vila J.A.; Scheraga H.A. Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures. Proteins 2008, 71, 641-654.
12.- Arnautova Y.A., Vila J.A., Martin O.A. and Scheraga H.A. What can we learn by computing 13Cα chemical shifts for X-ray protein models? Acta Cryst D 2009, D65, 697-703.
Funding
Supported initially by NIH (USA) grant GM-24893, and later by NIH (USA) grant GM-14312, and NSF (USA) grant MCB05-41633.
Support was also received from the IMASL-CONICET (Argentina), FONCyT-ANPCyT (Argentina) [PAV 22642 / 22672] and from the Universidad Nacional de San Luis (P-328501 / P-328402), Argentina.
The research was conducted using the resources of Pople, a facility of the National Science Foundation Terascale Computing System at the Pittsburgh Supercomputer Center (USA).