jCE/jFATCAT Structure Alignment Server V. 2.6

All vs All Protein Structure Comparison and Alignment

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History

Access to precalulated All vs All alignments.

You can get a beta release of the domain-based precalculated alignments from the new 3D similarity tab on the RCSB web site. The RCSB PDB production site currently provides chain-based precalculated alignments e.g. from here.

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.