Predict Binding Activity Of Ligands And Receptors From Dna Sequences

Question

[Jessica]

Hi all,

I have a list of ~800 ligand and receptor interaction pairs for a modelling purpose. I am seeking a way to score the probability of occurrence or strength of interaction of each pair. I was wondering if I could do this through multiple sequence alignment between the ligand and receptor sequences in a ligand-receptor pair. As we speak, I just start to learn basics of multiple sequence alignment, and I am not sure if my idea is even feasible. Any advice or suggestion is much appreciated.

Thank you in advance.

Wendy

[Flow]

if you start to work with sequences, you mean that all your ligands are peptides?

[Jessica]

Hi flow,

Thank you very much for your reply. Yes, all my ligands are peptides. Before your question, I did not realize that peptide and non-peptide ligands have different binding mechanisms. Are there any other differences between peptide and non-peptide ligands in terms of ligand-receptor interaction?

Going back to my question, given all my ligands are peptides, do you have any further guidance?

Thank you very much.

Wendy

[Flow]

it would depend on their chain length; for small peptides (less than 3 or 5) you could use protein-ligand docking methods, but for bigger peptides you could use protein-protein docking peptides, IMO

Answer 1

[Vladimir Chupakhin]

There is specific term for this - chemogenomics. Also try to look at the Connectivity Map approach.

[Jessica]

Thank you so much chupvl.