Open labarba opened 3 years ago
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Abstract: we went from 342 words in bd34595 to 215 in 1c9c671
Reviewer 1 expressed concern that the featured use case in the article is of “questionable value: the solvation energies of very large molecules.” In our response to this question, we explain that structure-based computations (like solvation energy) are still valuable for large molecules: researchers may run ensemble computations with many conformations, for example, to obtain an energy landscape. The central point of our software platform is that it provides high researcher productivity in these settings, where sets of experiments can be run from Jupyter notebooks, allowing short dynamics simulations coupled with solvation energy calculation. The use cases are varied: computing binding energies of large molecules, ensemble calculations, coupled short dynamics with structure-based analysis. The point is these investigations are facilitated by the interactive-computing environment, powered by high-performance algorithmic engines. The Zika virus case demonstrated that our software can handle virus-scale computations and the performance is on par with other well-optimized PB codes. We have added to the discussion to clarify this point, as detailed in the reviewer response.
While we ask you to address all of the points raised, the following points need to be substantially worked on:
Referee 2 provided the following references via email (regarding their major concerns 1 and 2):
https://pubmed.ncbi.nlm.nih.gov/26874202/ -- Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1610-8. doi: 10.1016/j.bbamem.2016.02.007. Epub 2016 Feb 10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278654/ https://pubs.acs.org/doi/10.1021/acs.jpclett.8b02298 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456034/
https://science.sciencemag.org/content/370/6513/203 https://www.nature.com/articles/s41586-018-0396-4
Referee 3 provided the following information/references via email (regarding their concerns 3 and 4):
[x] Concern 3) Grid refinement validation should be carried out for a large set of realistic biomolecules in terms of various evaluation metrics.
[x] Concern 4) Examples of other methods:
Li, A. and Gao, K., 2016. Accurate estimation of electrostatic binding energy with Poisson-Boltzmann equation solver DelPhi program. Journal of Theoretical and Computational Chemistry, 15(08), p.1650071. Nguyen, D.D., Wang, B. and Wei, G.W., 2017. Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies. Journal of computational chemistry, 38(13), pp.941-948.
You will also need to make some editorial changes so that it complies with our Guide to Authors at https://www.nature.com/natcomputsci/for-authors .
In particular, I would like to highlight the following points of our style:
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