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)

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FIND Find structural alignments by selecting from ALL or REPRESENTATIVES from the PDB.
CALCULATE Calculate structural alignment for TWO CHAINS either from the PDB or uploaded by the user. 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]
ALL and REPRESENTATIVES databases correspond to PDB of 2001-10-17.

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.

This service is a resource of the National Partnership for Advanced Computational Infrastructure (NPACI) and the National Biomedical Computation Resource (NBCR).

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