SALAMI: Structure ALignment And Match Inquiry



Hi there,
We are working on a new dramatically improved version of the SALAMI server. If you're feeling adventurous, you can try it out.
Title
eMail
Query structure upload
OR pdb ID/chain (e.g. 1cdk A)

   
SALAMI aligns your structure to every chain in the pdb90 library and returns a list of the most similar chains, their coordinates superimposed onto the query structure, and detailed alignments of your structure and the best matches. Soon, the structure library will be updated and kept in sync with the official pdb90.

Here, you can submit a pdb file to our server and specify the number of matches, alignments and structures you would like to recieve. Results are sorted according to the "andrew score" in the last column which is the frac_dme value multiplied by the coverage of the alignment. The s tructures returned by Salami have been superimposed onto your query structure. The results will be emailed to the specified address. Depending on the size of your query structure and the load on our cluster, the search will take anywhere between 2 minutes and one hour. Typically, a search should take about 10 to 15 minutes.
Feel free to put this server through its paces, and let us know what you think of it. Feedback in the form of bug reports, feature requests and general comments is very much welcome and should be directed at margraf [AT] zbh.uni-hamburg.de

For testing purposes, you can simply submit the 1cdkA chain with the default parameters. Alternatively, you can just look at results of this example query.