my protein consist of 4 chains, A B C and D, my binding pocket is on 2 chains A AND C , can i delete the B an D for carrying out the docking studies, as my binding pocket lies on A and C chain?
Hello.
Yes, it seems that you can delete the chains. But, as docking is done specifying a docking box, I don't see any advantage on deletiong additional chains.
Ricardo
Hi, you can carried out your docking studies with chain which having active site residues, rest of these chains should be deleted.
Hello.
Yes, it seems that you can delete the chains. But, as docking is done specifying a docking box, I don't see any advantage on deletiong additional chains.
Ricardo
Dear Ayzeha,
As Ricardo suggested no significance of deleting additional chain, even i can extend the deletion part to specific chains except the residues you involve in Local Search Algorithm. But that will cause no change with and without those chains or part.
I want to delete the chain as their residues will also interaction with besides all strict conditions set for docking.
Dear Ayzeha,
Before deleting any of the chain first I would suggest you to go through all available literature resources. As you mentioned that the active site lies between chain A and C. first try to find out whether your protein of interest is active as a dimer or tetramer. Most of the proteins are active as a dimer specially in ADHs. So it is always well and good to have all detail information about protein of our interest. If your protein is also active as a dimer then you can delete remaining chains which are not involved in binding site.
Best of luck!!
Yes, surely you can delete those chains. But, as far as docking is concerned specifying a particular binding site or pocket. However, advantage on deleting any additional chains help only to create a fine pose or easiness in vision..
Dear Ayzeha,
I hope you got the solution till now. If not, then send me the protein at [email protected] . I will cut the protein according to your need and send you the corrected format for your perusal (Assuming the fact that the protein is not of confidential nature).
Regards,
Rajeev K Singla
SERB-Young Scientist
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology