Salami server - structure alignment

Welcome to our new version of the Salami 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
   


The server is able to find similar structures for a certain query structure out of the PDB structre pool. You can type in an PDB-ID or upload an own structure as a query. An example page for a result can be found here. It is the result of structure 1kntA.

In this version of the server we have added a filtering and visualization option as well as a seperate tab for pairwise alignments:
With the filter it is now possible to first calculate alignments of such structures that are most probable similar. It also displays results of the first calculated results. Stepwise results of structures that are less expected to be similar are calculated and displayed. With the advanced opition "filter" this method is applied.
To get an general idea of what structures have been found as results, the visualization option can be used. It plots the results according to two principal componants based on the pairwise alignment. This is an example of the visualization page. To enable the visualization please check the corresponding option in advanced options.
If you are interested in a pairwise alignment of two or more specific structures, select the tab next to "Salami Search".

In case something is not working, please inform us via E-mail. The old server can be found here.