I have modeled a protein, performed MD simulation and Docking studies. What are the other/additional computational study that can be performed further in order to target a high impact journal.
To make a high impact:
1. Find a problem.
2. Find a way to solve the problem.
3. Solve the problem.
4. Write about the steps 1-3.
If your target is to publish in high impact journals , then there are many journals which will publish anything for money.
Instead Focus on the quality of the work that you are doing. Read different journals and explore what they have done.
To make a high impact:
1. Find a problem.
2. Find a way to solve the problem.
3. Solve the problem.
4. Write about the steps 1-3.
Dear Puneet,
That will depend on what Journal you are aiming at. Best way is to look for your kind of work in those journals and see what amount of data they find enough to get a paper published. Else, there are so many other factors that influence the chances of getting published in 'high impact journal' despite good work. In your case, a clear and elaborate interpretation of your docking and MD simulation studies is much needed. Other than this, as you are working on a modelled protein, model evaluation techniques can also be applied. Besides, reviewers also look for MD simulation 'timescale' whether or not it make any difference.
Firstly, I agree with Martin that the issue of your focus must be how to solve the problem and should not arise from the method you have in your hand.
I assume you are studying protein-drug interactions. Therefore, it is very common to do quantum chemistry calculations on the small molecule drug (e.g. molecular orbitals Hartee-Fock or density functional theory, etc.). However, I believe this step is done prior to the MD in order to improve the accuracy of the topology.
Often researchers are satisfied with reporting "interaction energy" that can be extracted from the MD data. However, it is very different from free energy or what is usually called "binding energy". For free energy calculations you need to perform different kind of MD simulations at different conditions.
The reason people use multidisciplinary approach to solve a problem is to be more confident that whatever model they have actually represents reality with most accuracy. That model should be reproducible and stable. Since you already have an open mind for other methods, then do not exclude wet lab to answer the question/problem.
Yazan Haddad Martin Klvana many thanks for your wonderful suggestions!!
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