CheShift-2: graphic validation of protein structures

Summary: The differences between observed and predicted (13)C(α) chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason, we previously introduced CheShift, a Web server for protein structure validation. Now, we present CheShift-2 in which a graphical user interface is implemented to render such local flaws easily visible. A series of applications to 15 ensembles of conformations illustrate the ability of CheShift-2 to locate the main structural flaws rapidly and accurately on a per-residue basis. Since accuracy plays a central role in CheShift predictions, the treatment of histidine (His) is investigated here by exploring which form of His should be used in CheShift-2. Availability: CheShift-2 is free of charge for academic use and can be accessed from www.cheshift.com Contact: has5@cornell.edu; jv84@cornell.edu Supplementary information: Supplementary data are available at the Bioinformatics online.