how can i find binding site sequence of two protein together?

Question

[ali.kian.saei]

i want to find binding site sequence of two protein to each others.

in papers i didn t find any data but i want to find database which can help me

this sequence important for me for design inhibitor for this binding site of two proteins

Answer 1

[Mensur Dlakic]

If structures of your proteins are known, you can dock them together to get some idea about potential interacting interface. From there the mutagenesis may help you confirm or reject the docked model. If you don't have the structures of your proteins but there are similar structures available, you can do the same thing but first have to make homology models of your proteins.

Yet another option is to obtain a crystal structure of the protein complex.

If you were asking about an easy way of finding a protein binding interface, I am afraid that such a thing does not exist.

[ali.kian.saei]

thanks for your answers. i have pdb format of domain of my proteins but there isn' t any full structure of whole protein.

i try to find computational method for predict binding site.

Answer 2

[tothepoint]

I believe if you knew the binding site you can easily explore the sequence using PyMol. Although your question is little confusing.

[ali.kian.saei]

thanks for your answer.

but i know the domains (about 160 residue) that two proteins bind together but i want to know the sequence of two proteins that directly bind together.

thanks