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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

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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
Submission
[?] E-Thrifty results will be sent to the provided email address.
Email address must not contain special characters e.g. ( ) < > , ; : \ " [ ]


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