About E-Thrifty

The "Enhanced-Thifty" or E-Thrifty is a chemcial shift-based threading method, which uses sequence and chemical shift similarity as well as chemical shift-derived secondary structure, super-secondary structure and accessible surface area to identify and determine the most likely 3D structure that a query protein may have. Our tests indicate that E-Thrifty's performance is comparable to using coordinate data to identify structurally similar proteins via 3D superposition. E-Thrifty accepts BMRB (NMR-Star 2.1 or NMR-Star 3.1), SHIFTY and NEF-formatted chemical shift files and produces multiple output files. These output files include: 1) an alignment file showing the sequence - structure alignments for the top 10 hits; 2) a summary file containing alignment scores, chemical shift scores, e-value and the cluster membership associated with each hit; and 3) a 3D structure (PDB coordinates) of the query protein using the top scoring template (or multiple templates from the clusters) generated via MODELLER. If you use E-Thrifty please cite the following reference:

Reference: Noor E Hafsa, Mark V. Berjanskii, David Arndt, David S. Wishart, Rapid and Reliable Protein Structure Determination via Chemical Shift Threading. Journal of Biomolecular NMR (2017): pp. 1-19


Example To Test the Server
Example Protein Human ubiquitin, 76 residues, monomeric, coordinate error with respect to the reference model (PDB ID: 1UBQ) is 2.0 A

Chemical Shift Input
E-Thrifty accepts BMRB NMR-STAR 2.1 and 3.1 formats, SHIFTY and NEF formats.
See format requirements and examples

OR, Paste Chemical Shifts Below
IMPORTANT: If a file is selected for upload above, it will be used and content of the text box below will be ignored.

Correct Referencing Offset Correct Neighbor Residue Effect
Search Options

Example 1ubqA, 1d3zA, 2oedA
Modeling Options
[?] If checked, flexible tail regions will be ignored in modeling.
Note that, the HIS-tag regions will be automatically excluded.

Single Multiple

1 top model The top template will be used to produce a single comparative model 5 top models Top several templates will be used to produce multiple comparative models
[?] E-Thrifty results will be sent to the provided email address.
Email address must not contain special characters e.g. ( ) < > , ; : \ " [ ]