Databases and Tools for 3-D Protein Structure Comparison and Alignment

Using the Combinatorial Extension (CE) Method 

 

 

Structural similarity between Acetylcholinesterase and Calmodulin found using CE (Tsigelny et al, Prot Sci, 2000, 9:180)

 

 

Select from the following options by clicking the links on the right

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More Info

 

FIND

Find structural alignments by selecting from ALL(this mode is in the process of fixing, please use REPRESENTATIVES for now)  

 

Updated

2001-10-17

 

or  REPRESENTATIVES from the PDB.

Updated

2004-08-16

CALCULATE

Calculate structural alignment for TWO CHAINS either from the PDB or uploaded by the user.

Updated

2006-11-08

 

Calculate structural neighbors for one protein UPLOADED BY THE USER AGAINST THE PDB.
Calculate MULTIPLE STRUCTURE ALIGNMENT (at University at Albany, NY).

 

DOWNLOAD

Download the SOFTWARE and DATABASES used here for local use.

 

RESULTS

Review results from our own alignment experiments: SUBDOMAINS [pdf] | PROTEIN KINASES [pdf] | ESTERASES, LIPASES [pdf]

 

 

 

 

CE resource is relying on STRAP  for a number of services it provides.

Citing the use of this resource

Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 11(9) 739-747.

Contacting the authors

shindyal@sdsc.edu - Ilya N. Shindyalov; bourne@sdsc.edu - Philip E. Bourne

Acknowledgements

This work was supported through grants DBI 9630339 and DBI 9808706 from the National Science Foundation.

Funded in part by NIGMS GM63208

 

This service is not funded as part of the Protein Data Bank (PDB).