3-D Protein Structure Comparison and Alignment


Annotation & Function


This website has databases and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method.


The Combinatorial Extension (CE) method utilizes an algorithm that builds an alignment path between two protein structures using aligned fragment pairs (AFPs). It is these AFPs, one from each protein and based on local geometry, that confer structure similarity. Combinations of the AFPs represent possible continuous alignment paths. These paths are selectively extended or discarded, which leads to a single optimal alignment. This method is fast and accurate and is suitable for database scanning and analysis of large protein families. This resource is particularly useful for studying proteins of unknown function. A relationship between two proteins of similar structure might be inferred where a sequence alignment may not have yielded this information.

One-on-one alignments and searches can be performed against all structures in the PDB or a representative subset from the PDB or structures uploaded by the user. In addition to running comparisons on the server, users can download the software and databases for local use. For more information, see the website at http://source.rcsb.org/jfatcatserver/ceHome.jsp.



CE home page.


Shindyalov IN, Bourne PE. "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path." Protein Engineering 11:739-747 (1998). PubMed ID:9796821

Shindyalov IN, Bourne PE. "A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm." Nucleic Acids Res. 29: 228-9 (2001). PubMed ID:11125099 | PMC Link


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


Free full text of the Shindyalov article is available at http://binf.gmu.edu/vaisman/csi731/proteng98-ce.pdf


share on Facebook Tweet This share on LinkedIn add Google Bookmark add to delicious Share on reddit share on StumbleUpon Digg this

Last edited:Mon 26 Aug 2013 - 3 years, 7 months ago