ET Viewer
Input a PDB identifier directly (for example 1f88) to visualize with the ET Viewer.
The ET Viewer provides:
An ET Wizard that automatically performs ET analyses starting from PDB file names, or actual PDB formatted files, as input, and yielding an .etvx file of the relative ranks of evolutionary importance of each sequence residue as output. The Wizard lets you adjust the parameters of ET runs through the ET Wizard interface.
A molecular graphics display that reads the .etvx files and produces a colored structural map of the importance of each residue in the protein. Typically, top-ranked residues will cluster significantly (as assessed by a z-score), and reveal functional sites that become evident as protein surface areas with a high density of top-ranked residues. The alignment and the evolutionary tree used as input to the ET can also be shown.
All the data files produced by the ET Wizard can be downloaded.
Licensing
The Evolutionary Trace viewer is freely available for non-profit use. The current release has only been tested thoroughly on Windows XP. For profit use of the Evolutionary Trace Server may be arranged by contacting Terese Rakow ( trakow@bcm.tmc.edu, 713-798-6821 ) to request a license from Baylor College of Medicine.
Citing ET Viewer
If you intend to use the Evolutionary Trace Server and Viewer as part of a published work, cite the following papers:
Morgan, D.H., D.M. Kristensen, D. Mittleman, and O. Lichtarge. ET Viewer: An Application for Predicting and Visualizing Functional Sites in Protein Structures. Bioinformatics. 2006 Aug 15;22(16):2049-50. Epub 2006 Jun 29.
Mihalek, I., I. Res, O. Lichtarge. (2004). "A Family of Evolution-Entropy Hybrid Methods for Ranking of Protein Residues by Importance" J. Mol. Bio. 336(5): 1265-82.
Lichtarge, O., H.R. Bourne and F.E. Cohen (1996). "An evolutionary trace method defines binding surfaces common to protein families." J. Mol. Biol. 257(2): 342-58.