CheShift

From Wikipedia, the free encyclopedia
Jump to: navigation, search
CheShift-2
output of CheShift-2 red colored residues are flaws that should be
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-2 (pronounced /tʃeʃɪft/) is an application created to compute 13Cα and 13Cβ protein chemical shifts and to validate protein structures. It is based on quantum mechanics computations of 13Cα and 13Cβchemical shift as a function of the torsional angles (φ, ψ, ω and χ1, χ2) of the 20 amino acids.

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.[1] 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.[2]

CheShift-2 can be accessed online at http://www.cheshift.com, or via PyMOL plugin.

See also[edit]

Related software[edit]

External links[edit]

References[edit]

  1. ^ Martin, O. A., Vila, J. A. and Scheraga, H. A. (2012). "CheShift-2: graphic validation of protein structures". Bioinformatics. doi:10.1093/bioinformatics/bts179. 
  2. ^ 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. doi:10.1073/pnas.1315525110.