PNMAVis: Visual Analysis Tool of Protein Normal Mode for Understanding Cavity Dynamics

Round 1

Reviewer 1 Report

 

In this work, a novel interactive visualization tool to better understand cavity dynamics is presented. The tool is interesting and described in detail, making this work a valuable contribution. The paper can however be improved to make it read more fluently (several sentences need to be checked, also see below). By improving some basic definitions the paper could also be made more accessible for people that are less familiar with the topic.

 

-          Line 7-8: “reduce the exploration and access to complex data”: confusing; best to rephrase

-          Something appears to have gone wrong with the references, as the first citation I see in the text is reference 5 on line 36 (I don’t see references [1-4] cited in the text before [5]). I would in particular expect to see a couple of references on line 28 and 31.

-          Line 32: perhaps indicate the order of magnitude that can be simulated.

-          The colors need to be explained in the caption of Figure 1.

-          Line 120: reference needed after “Doruker et al.”

-          Line 119-125: this general explanation needs to be improved

-          Check line 131: “José …”

-          The construction of the sentence on line 139-141 needs to be corrected.

-          Line 151: “the grid-based are not suitable” -> the grid-based methods are not suitable

-          The principle of the Voronoi-based method needs to be explained

-          “Our data preparation generates pipeline is summarized as follows” -> "generates" needs to be removed

-          Check capital letter K in Equation (3)

Mention the color definitions in the caption of Figure 9.

Author Response

Please find the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

This study investigated the “PNMAVis: Visual Analysis Tool of Protein Normal Mode for Understanding Cavity Dynamics”. The current format needs a major revision and cannot be published at this stage;

Comments:

Ø  The novelty of this work is not highlighted. This needs to be clearly explained. What was the hypothesis? How the results can support the hypothesis?

Ø  Abstract needs to be rewritten. Novelty should be mentioned in the abstract. Abbreviations should not be used in the abstract. Abstract should be clear in a way that even without reading the whole paper, it still can give some useful information.

Ø  The authors should mention the dependent and independent variables with units in Figures 4, 5, 6, 7, 11 and 12. The authors should also format axis of the figures to improve the quality of manuscript for readers.

 

Author Response

Please find the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The authors done well in revision and meet most of the comments.

Author Response

Attached is the revised manuscript.

Author Response File: Author Response.pdf