The molecular docking was performed by redocking the co-crystallized ligand and validating the protocol by finding the RMSD of the docked ligand by superimposing it on co-crystalized ligand. Afterwards the docking was performed on new set of ligand library. But can we justify the results of docking without doing md simulations? If yes, then please provide a reference from article.
Yes, it is possible to present docking results without additional support from the results of molecular dynamics (MD) simulations. However, increasingly, reviewers of manuscripts under consideration for publication in journals are requesting MD simulations to help bolster conclusions derived from docking results. It is, of course, also helpful (and often necessary) to have experimental results pertaining to the binding of ligands to macromolecular targets and to use docking and/or MD simulations to provide explanations for the observed experimental results.
I like to add one point: using one ligand may not be an accurate strategy giving that the docking is challenging. I recommend to use multiple protein-ligand complexes with varying ligand sizes and then redock, check RMSD and plot those values. This way you can estimate the error rate in docking w.r.t the ligand size. This will be helpful for the justification of your docked complexes with unknown ligands.
Yes, it is possible to go without MD, but not recommended. Even a short MD will give better chance for publications. And do not do MD for every complex, just the top 1-3 complexes or your complex of interest.
Using more than one software/algorithm is also recommended. There are multiple web servers are available nowadays, that can carry out these tasks.
Molecular docking has some limitations, such as the assumption of rigid receptor and ligand structures, the neglect of solvation effects, and the uncertainty of scoring functions. Therefore, molecular docking results may not always reflect the true binding mode and affinity of the ligand-receptor complex. as reviewers, we recommend that authors supplement their docking study with molecular dynamics simulations, MM-PBSA and
Per-residue decomposition analysis.
Dear Masooma Khan first, It depends on the reviewer and journal where you have submitted the manuscript.
If the study is completely based on in silico methods you need to preform MD Simulations if you are aiming for high impact journals.
If you cannot do that then based on my experience, I would suggest you can preform multiple docking experiments using different algorithm based programs to justify your hit potential. Moreover you should use highly active compound or drug already know against the target during the docking study for comparative study.
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