jCE/jFatCat Local Database Search

Run a Local Database Search.

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Database Searches User Interface

On this page, you can open up a User Interface that allows to run local database searches.

Click here to Start the DB Search User Interface using the Java Web Start technology.

The application will communicate with the RCSB web site and fetch a recent version of the representative PDB chains, clustered for 40% sequence ID. The PDB chain specified by the user will be compared against these representatives.

To have more control what is being compared against, download jCE/jFatCat and run a local DB search.

Contacting the Authors

Acknowledgments

The original version of CE was developed by Ilya Shindyalov and Philip Bourne through grants DBI 9630339 and DBI 9808706 from the National Science Foundation. The current jCE version is maintained as part of the RCSB Protein Data Bank (PDB) which is funded by NSF grant DBI 0829586
The original FATCAT code was developed by Yuzhen Ye & Adam Godzik.
Web site design: Bojan Beran

Citing the Use of This Resource

Reference:
Precalculated Protein Structure Alignments at the RCSB PDB website
Andreas Prlic; Spencer Bliven; Peter W Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne Bioinformatics 2010; doi: 10.1093/bioinformatics/btq572
CE Reference:
Shindyalov IN, Bourne PE (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Engineering 11(9) 739-747.
FatCat Reference:
Yuzhen Ye & Adam Godzik (2003)
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Bioinformatics vol.19 suppl. 2. ii246-ii255.