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Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode of docking that I found through the simulations, and how it is consistent with available experimental evidence. The point is that my paper wouldn't have any new experimental evidence. Rather, I analyze existing experimental evidence in the literature and demonstrate that the model of interaction I propose explains this data. Are there respectable journals accepting this type of research? Can you post some example journals like this?

Also, can you post some references to good papers like these, hopefully highly cited, if there are any?

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  • $\begingroup$ Several journals accept publications like this. The questions to ask are which biological audience would be most interested in the results and the expected impact of the results. Once you know these it is easier to narrow the journal search. $\endgroup$ – Darwin Jul 10 '15 at 20:33
  • $\begingroup$ @Darwin Can you put some examples of journals? (And, if you have it, along with the impact points) $\endgroup$ – becko Jul 10 '15 at 20:37
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    $\begingroup$ @becko Be careful about relying too much on journal impact factors (JIFs): yes, Nature Cell and Science do publish great research, but an article isn't necessarily great (or even decent) just because it's in one of those journals. $\endgroup$ – Daniel Standage Jul 10 '15 at 20:42
  • $\begingroup$ @DanielStandage Of course. But the impact factor does relate to the visibility of the paper. $\endgroup$ – becko Jul 10 '15 at 20:44
  • $\begingroup$ @becko only very loosely. Many people regard it as a made up number that's doing more damage than good. Even the chief editors of cell and nature are wanting new bibliometrics. $\endgroup$ – James Jul 10 '15 at 21:03
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Protein-protein interactions is an area of biophysics, so certainly Biophysical Journal (published by Cell) is a nice place to look.

PNAS has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence.

The Journal of computational chemistry certainly about a lot of simulations and modeling, so see for yourself.

As for publications, the fact that you are asking for references makes me think you haven't done your homework on literature review, as it is always first and foremost job in a research project.

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  • $\begingroup$ I'd also recommend having a look which journals of the papers you have read and are citing have been published in. You will probably have to make a call whether you want to publish in a more methods-based journal (bioinformatics in your case) or in a more topic-based journal (biology/biochemistry/biomedicine...) $\endgroup$ – Gerhard Jul 11 '15 at 10:34
  • $\begingroup$ +1 Good answer. I am still deciding whether I'll begin this research project and which direction to take. I haven't found papers that are entirely "theoretical", in the way that I describe (although they support available experimental evidence published elsewhere). If you know any please post the reference. $\endgroup$ – becko Jul 11 '15 at 15:15

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