Welcome to PreSSM web interface

This web interface matches the predicted secondary structures in a protein given it's sequence with secondary structure in the protein's 3D model given it's atomic coordinates.

Users can get secondary structure prediction from either of PSIPRED, CFSSP and NSPA servers. The assignment of secondary structure is based on STRIDE (Structural identification), an algorithm for the assignment of protein secondary structure elements given the atomic coordinates of the protein.

We Require some inputs

Select a method to predict secondary structure. Clicking on names will redirect you to the server. Once there, copy and paste your protein sequence as instructed. To know more about these servers visit our references section.

In case of RaptorX you need to download zip file and use the file seqid.ss3_simp.txt by pasting the content in the textarea below. In case of PSIPRED you need to download Horiz format output file and paste the content in the textarea below. For rest of the two, just copy and paste the resulting alignments displayed on webpages in the textarea below. For more information on how to get and copy prediction follow ReadME document.

Now you need to copy and paste the atomic coordinates of protein's 3D model in the textarea below. Make sure that coordinates are of the same protein as given for prediction.

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