CheShift

CheShift-2

Stable release|

3.0 / 1 September 2013 (2013-09-01)

Written in| Python, HTML
Operating system| Cross-platform
Available in| English
Type| Bioinformatics
License| Free of charge for academic use
Website| cheshift.com

CheShift (pronounced /tʃeʃɪft/) is a bioinformatics software tool used for the prediction of protein nuclear magnetic resonance (NMR) chemical shifts and the validation of protein structures. The software operates as a web server and as a plugin for the molecular graphics program PyMOL. It is primarily used to assess the quality of experimentally determined or computationally predicted protein models by comparing their theoretical chemical shifts with observed values.

## Contents

* 1 Principle
* 2 Versions
* 2.1 CheShift-2
* 2.2 Related software
* 3 See also
* 4 References
* 5 External links

## Principle

The core principle of CheShift is based on quantum mechanics calculations. It predicts the chemical shifts of carbon atoms in the protein backbone (13Cα and 13Cβ) as a function of the torsional angles (φ, ψ, ω and χ1, χ2) of the 20 amino acids.

## Versions

The original CheShift server was introduced in 2009. In 2012, an updated version named CheShift-2 was released. This version introduced several key improvements, including the prediction of 13Cβ chemical shifts in addition to the original 13Cα shifts, providing more data for validation.[1]

### CheShift-2

CheShift-2 can return a list of theoretical chemical shift values from a PDB file. It also can display a 3D protein model based on an uploaded PDB file and chemical shift values. The 3D protein model is colored using a five color code indicating the differences of the theoretical vs the observed chemical shifts values. The differences between observed and predicted 13Cα and 13Cβ chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures.[2] If both 13Cα and 13Cβ observed chemical shifts are provided CheShift-2 will attempt to provide a list of alternative χ1 and χ2 side-chain torsional angles that will reduce the differences between observed and computed chemical shifts, these values can be used to repair flaws in protein structures.[3]

CheShift-2 can be accessed online or via PyMOL plugin.[4]

### Related software

* WHAT IF software
* PROCHECK
* PSVS

## See also

* Structure validation
* Bioinformatics
* Computational biology

## References

1. ↑ "Changelog - CheShift". http://cheshift.com/changelog.
2. ↑ Martin, O. A., Vila, J. A. and Scheraga, H. A. (2012). "CheShift-2: graphic validation of protein structures". Bioinformatics 28 (11): 1538–1539. doi:10.1093/bioinformatics/bts179. PMID 22495749.
3. ↑ Martin O.A. Arnautova Y.A. Icazatti A.A. Scheraga H.A. and Vila J.A. (2013). "A Physics-Based Method to Validate and Repair Flaws in Protein Structures". PNAS 110 (42): 16826–16831. doi:10.1073/pnas.1315525110. PMID 24082119.
4. ↑ "Cheshift - PyMOLWiki". https://pymolwiki.org/index.php/Cheshift.

## External links

* Official website
* CheShift PyMOL plugin
* GitHub repository
* http://www.cheshift.com

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