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LaJolla is a peer reviewed algorithm for the 3D alignment of RNA and protein structures (see our gallery)

There are excellent algorithms known for structural protein / RNA alignment, but LaJolla is different in many regards:

  • LaJolla uses an indexing technique that virtually allows to screen thousands of structures within minutes.
  • LaJolla is peer reviewed (see below) and it can be shown that it is at least as good as leading algorithms in the field of RNA and protein alignment.
  • LaJolla is open source and platform independent. You can use the software freely. You can look into the code. You are part of the project making LaJolla better with each and every suggestion!

If you use LaJolla in your research please cite: Bauer, R.; Rother, K.; Moor, P.; Reinert, K.; Steinke, T.; Bujnicki, J. M.; Preissner, R. Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2009, 2, 692-709. open access full text

Feedback heavily welcome :) drop us a mail at our public mailing lists (users / developers)

Latest News


Documentation and Tutorials

Additional stuff

  • Some eye-candy alignments of LaJolla in our gallery
  • datasets used for benchmarking link
  • The github project page with all development stuff - pull requests welcome!


  • krother
  • marcusschroeder
  • pm petmoo
  • reyez (aka ra)

Institutional Support

  • International Institute of Molecular and Cell Biology in Warsaw, PL
  • Structural Bioinformatics Group, Charité Medical University, Berlin, DE [1]
  • Institute of Molecular Biology and Bioinformatics, Charité Medical University, Berlin, DE [2]
  • International Graduate School: Genomics and Systems Biology of Molecular Networks, Berlin, DE [3]
  • Special thanks to the BioJava team for providing an excellent bioinformatics library!

old news

  • 2009-08-05 LaJolla talk SDSC in San Diego / Group of Phil Bourne
  • 2009-07-26 LaJolla won a talk at the IWSB 2009 in Boston, USA
  • 2009-06-25 LaJolla is on show at the ISMB / ECCB 2009 (Poster W041).
  • 2009-04-22 jippeee! we got published in Algorithms! check out the paper!!!
  • 2009-03-05 new release 2.1! (with symmetric scoring :) ) download!
  • 2009-03-05 new final release of LaJolla 2.0 is available.
  • 2009-01-25 new release 2.0-beta2 check it out.
  • 2009-01-05 work for version 2 has begun; check out the Roadmap!
  • 2008-12-03 new release (0.4.0) => faster protein alignment / less memory consumption, many improvements) => download!
  • 2008-11-05 new release (0.3.1) more command line options, fuzzier default values, new alignment method
  • 2008-10-31 new release (0.3.0) adding support for RNA eta theta angles check it out!Suite codes
  • 2008-10-28 new release adding support for RNASuite codes
  • 2008-10-26 new minor release fixing a bug that omitted finding 100% identical chains
  • 2008-10-22 hoorrrrraaay! first public release... also check out the ProteinTutorial!
  • 2008-10-11 first working 3D alignments. yea!
  • 2008-08-xx testing evaluating testing
  • 2008-08-11 marcusschroder joined the team for the RNA mining


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