input: amino acid sequence
output: potential protein binding partners to sequence
Thanks for taking the time to address my question.
Bre
Dear BreAnne MacKenzie,
I think you can do it using https://string-db.org/ and then you can select your search for "Protein by Sequence".
Best regards,
Leite
Hi BreAnne, protein-protein interactions are difficult to predict because their interactions can be dependent on their 3D conformations and not their linear amino acid sequences.
Dear BreAnne,
You may find somehing interesting for you here:
http://www.uwm.edu.pl/metachemibio/index.php/protein-ligands
With best regards
Piotr
Dear BreAnne,
actually, it's highly difficult to predict an interaction between two proteins because, as said Steingrimur, it might be strongly related to the 3D structure.
However, there is case for which it becomes a bit less difficult: when the protein binds to a linear motif. A motif is a short amino acid sequence (of about 3 to 6 residues). In this case, the interaction is mostly driven by the sequence since the motif is unfolded most of the time.
You may find interesting details at the ELM website (http://elm.eu.org/), which stands for Eukaryotic Linear Motif. It's a manually curated database based on literature. You enter a protein sequence and you'll see all the putative motifs bound to it. Then it's also possible to search for a special motif if you already know it.
Best regards
Yves
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