If it happens that during your homology modelling and MD study of such protein, other authors published the x-ray crystallographic structure of the same protein. What should be done? can you publish your own computational study on the same protein though it already solved by x-ray crystallography before your computational findings submission?
If you've already submitted your paper, and the experimental findings do not contradict your result, you would add a note referring to to the experimental structure in a "note added in proof". If you are not yet at that stage, you should carefully assess whether you can derive any added value from the fact that you have performed a dynamics simulation. Do you have a purely computational study, or does it also relate to and attempt to explain experimental findings?
You can check out these articles. The second had a similar scenario like yours.
1. Article Structure and drug resistance of the Plasmodium falciparum t...
2. Article Structural and evolutionary analyses of the Plasmodium falci...
Annemarie Honegger , I am writing my draft right now in 2020 and it been one year since I started my project. The crystallographic structure of the same protein published in October 2019. My calculation fully based on Homology modelling and Molecular Dynamics simulation which is literally fully computational approach.
Paul Awolade , Your suggested papers really giving me a source of light on the darkness.
I would like to express my thankfulness to all of you for your valuable instruction and a blissful solution for this type of critical problem. From your suggestions, finally, I got relieved that my last one-year calculation is not becoming a waste of time, though I gave up and planning to exclude that protein from my project which faced this type of issue. Now I am confident and I will discuss all those matters in my draft comparing with the published article.
It happened to us when we were studying the zika virus proteins. We superimposed our structure to that of published structure and compared the results . The reviewers might ask you to do the same.
Dear Shamrat,
You can complete your study and send it to press as a computational outcome. If your main findings were just a prediction of the structure then you lost the priority but when you include the comparison the experimental structure then it serves as a useful reference. It happened several times to me that I completed a computational project, predicted the structure, the structure was solved and my model was better than X-ray structure. I worked on many proteins from the PDB that were erroneously solved. So if you only have independent findings, do not worry just publish. Everybody understands that modeling is a "softer" technique but that serious errors happen in experimental structures. So even though the modeling is softer it has positive contribution. However, in such a case you must select the journal carefully, be lucky with editors and the referees.
Good Luck.
Bog
Hello, I think you can still publish your results, but it might be challenging to convince the editors, reviewers and readers that it is useful. You should not ignore the experimental structure, this will only show your incompetence in the field. My advice is to compare your model with experimental X-ray structure and critically analize where it corresponds and where it does not. Put focus on dynamic studies, since crystal structure is always just a snapshot of the moving system. Check if you have conformation similar to experimental among your MD snapshots. Do MD with crystal structure using the same settings as for HM and compare. Mind also the ligand if any. Find conclusions which can be useful for researchers in this field and highlight them.
Hi Shamrat,
I agree with Jelena Melesina . It would be better if you could supplement some dynamic data or predict the interaction with the ligand.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics