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FATCAT Pairwise Alignment

FATCAT Home Pairwise Alignment Database Searching Structural Neighbors References Help

What does FATCAT report? See a sample report

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Get the 1st structure (please use only one method from the 3 methods below):
Enter a name for your structure:   (optional)
  • Upload file (in PDB format):    
  • or   Provide PDB code:      Chain:  
  • or   Provide SCOP domain code:  
Get the 2nd structure (please use only one method from the 3 methods below):
Enter a name for your structure:   (optional)
  • Upload file (in PDB format):    
  • or   Provide PDB code:      Chain:  
  • or   Provide SCOP domain code:  
(Note 1: You can either upload local PDB files or simply provide PDB codes (eg. 1abo) or SCOP domain code (eg. d1mt0a_))
(Note 2: FATCAT server will automatically download the PDB files from RCSB when PDB codes are provided or from SCOP if domain 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)

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


FATCAT Reference: Y. Ye and A. Godzik "Flexible structure alignment by chaining aligned fragment pairs allowing twists" Bioinformatics, 2003, 19(Suppl 2):II246-II255

Other Servers | Godzik Laboratory | The Burnham Institute,
Contact: FATCAT

The initial version of this website was developed by
NSF grant DBI-0349600 and NIH grant GM63208

Current support provided by
NIH grant P20 GM076221 - Joint Center for Molecular Modeling (JCMM)

First set up: Jun 22, 2004
Last update: Jan. 31, 2008