TOPS++FATCAT Home Database Searching References Help FATCAT Godzik Lab

WARNING: this web server is no longer updated and maintained. The last update is 2008.

NEW: Please go to http://fatcat.godziklab.org instead which is weekly updated.

TOPS++FATCAT Similarity Search

This server performs the TOPS++FATCAT similarity search for a given protein structure against a database
and provides the top hits of similar structures.

Structure pairs with P-value < 0.05 are significantly similar. Check here for a sample report.


Your email: (required, a notice will be sent to you by email once the search is done)

Get your structure: upload file (in PDB format) or provide PDB code Chain Name
(Note 1: You can either upload local PDB files or simply provide PDB codes (eg. 1abo))
(Note 2: FATCAT server will automatically download the PDB files from RCSB when PDB codes are provided)
(Note 3: If your PDB has more than one chain AND you do not want to use the 1st chain, please define the Chain; otherwise, the 1st chain will be used)
(Note 4: Type in "zero" instead of "0" for chain 0; the server will not recognize 0)

Select a database to be searched against

Alignment model (when rigid is selected, TOPS++FATCAT is forced to run rigid comparison)



TOPS++FATCAT Reference: Mallika Veeramalai, Yuzhen Ye and Adam Godzik. "TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model" BMC Bioinformatics ,9:358, 2008.


Contact Us | TOPS++FATCAT | FATCAT | Other Servers | Godzik Laboratory | The Burnham Institute

This research was supported by NIH grant P20 GM076221 JCMM (Joint Center for Molecular Modeling)

Locations of visitors to this page