Salami search server

it finds the most similar structures according to your input structure by multiple structure alignment

currently in structure pool - clusters : 120.139

Welcome to our current version of the Salami search server!

Title
E-mail
Structure upload
or
PDB ID, chain
or
List of PDB IDs
Advanced options>>> rmsd thresh min fracDME max number of items filter by focf visualize distances protein angles (φ,ψ) (θ,τ)
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Given a query structure, the server will look for similar structures in the protein data bank (PDB). The query can be a known structure or you can upload your own coordinates in old-fashioned PDB format. We do not read mmcif yet. There are some example results for 1knt A here. We have added filtering and visualization options. Please choose one or neither of the options. They do not play well together. Additional we have a seperate tab for pairwise alignments.

Filtering
The focf filter does a pre-ranking of candidates. Alignments are first calculated for proteins most likely to be similar and these are shown first.

Visualization
To get a general idea of what structures have been found, try the visualization option. It spreads the protein homologues in a 2D space using the first two principal components from a similarity matrix of hits. This is an example of the visualization page.To enable the visualization please check the box in advanced options. If you are interested in a pairwise alignment of two or more specific structures, select the tab next to "Salami Search".

Depending on the size of your query structure and the load on our cluster, the search could take from 5 to 180 minutes, but typically a search takes 10 to 15 minutes. You don't have to wait long and additionally you receive an email when the results are ready.
If something is broken, please do not hesitate and send an email (Martin Mosisch ). Old server