Input protein structure Motif Search

[dbg08899r]

Dear Steinegger lab,

Thank you for creating such amazing web server!

I have a question regarding the input in the section of Motif Research. Let's say I want to search a different motif for a determine protein. My protein is called "X", so, I downloaded the .pdb of X and upload in the section of Motif Search, and in the "Selected Motif" section, I include some positions from my pdb that are of my interest for replacing with other similar without altering the protein structure.

Let's say I want to have an alternative motif for: AGCAGCAGC.

So, I just need to include the coordinates for each atom from my .pdb file for that AGCAGCAGC motif in the "Selected motif" section, right?

I would like to keep some important binding motifs for that X protein, do I need to specify them as well?

The issue is that I have been doing both ways:

• including in the "Selected motif" just the motif I want to replace to find a similar one,
• including just the binding motifs I want to keep for my X protein.

But for both ways, I got similar results, and I don't get a similar motif, but always the same from the one I want to replace.

But I'm wondering actually, which is the right way to do it? Thank you so much in advance for your time and help.

Best,
dbg08899

[martin-steinegger]

Thank you for your kind words and for using Folddisco!

Folddisco is designed to search for structural motifs within a database using the residues that you select from your uploaded structure. It does not perform residue replacement or structural modification. Folddisco can search for residue substitutions (in default it does not, see Extended search), the syntax is supported in the webserver, additionally it allows more angle or distance divergence but these parameters are currently only support at the stand alone version.