Hi all, I am working on the protein-protein interaction study. The homology modeling protein structure was in good quality which Ramachandran plot shown more than 97% of aa are in the most favoured region. In addition, the sequence similarity is high which is about 70% similarity to the reference crystal structure. Hence, I proceed to protein-protein docking, which docked the homology protein structure (receptor) with another protein crystal structure (ligand). I have generated a set of molecular interaction data and is going to publish the works. However, I found that most of the journal will require MD. Is there any journal that can accept the molecular docking data without MD?
What is the meaning of MD, a medical degree or melocular dynamic, or something else? Here is journal example referred the molecular dynamics (MD) answer:
1. Journal of Molecular Graphics and Modelling
2. Bioinformatics
3. Journal of Chemical Information and Modeling
4. PLOS Computational Biology
5. BMC Bioinformatics
6. Briefings in Bioinformatics
7. Journal of Theoretical Biology
8. Proteins: Structure, Function, and Bioinformatics
Hope this help you well.
It would be difficult to publish a study that involved only docking without substantial additional computational and/or experimental laboratory results. Moreover, protein-protein docking is particularly problematic, especially if one of the docking partners is a homology model. Regarding the assessment of the quality of protein structures, there are additional criteria to consider beyond a Ramachandran plot -- I suggest using the Molprobity server to get a more complete evaluation. In addition, for protein-protein complexes, consider using AlphaFold multimer or AlphaFold3.
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