I have used CycloPs and ACD/chemsketch to generate virtual structure of peptide (pdb format). Is it necessary to optimize the structure or do energy minimization studies before proceeding to docking studies? I want to optimize the structure and then dock the peptide with cancer-related proteins. Can someone tell me how to proceed?
Dear Abheepsa,
I think the best method for optimization of your structure is quantum mechanic methods like B3LYP,.... so the best choice for you is Gaussian package.
HAH
Octapeptide is a rather large structure having multiple local minima. You can try to use some sort of annealing protocol, like replica exchange over a wide temperature range. But no the guarantee of finding the true minimum.
I would try a protocol like this http://www.biomolecular-modeling.com/Abalone/Protein-folding-Chignolin.html , but in the AMBER99SB or AMBER03, and with a lot of replicas, and in a greater range of temperatures.
You might want to have a look at the papers published by EA Coutsias on generating conformational ensembles for protein loops and cyclic peptides - see for example http://www.ncbi.nlm.nih.gov/pubmed/21743800
Actually it will depend on the docking procedure you choose, if you give full liberty of movements to the ligand (the octapeptide) it is indifferent if you optimize the structure of the peptide prior to docking. On the other hand if you are going to treat the ligand as a rigid structure during docking then you should optimize the structure (although for peptides won't be easy).
Hello Abheepsa, It is recommended that you optimize your structures before proceeding for docking. The bonds between atoms might not be perfect and molecules may not be energetically stable, so optimization becomes necessary. The tool will provide/optimize molecules the best energy score and stability which can further be used for docking.
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