A Concise Review of Biomolecule Visualization

Round 1

Reviewer 1 Report

The paper by Li and Wei provides a comprehensive review of the history and current status in the area of biomolecular visualization. This review is well written and organized and the Figures and Tables are very useful. I enjoyed very much reading the manuscript and I am sure it will be a valuable resource for researchers from various disciplines. As a biophysicist using biomolecular visualization software extensively, I will certainly distribute this review to my students and collaborators after publication.

I have one suggestion for improvement. I find the caption of Figure 2 confusing. The caption says 'different representation models of ribonucleic acids', but the displayed PDB structure (1m07) is actually an RNase enzyme with only a short fragment of RNA. Also it would be better if the caption refers to the panels (A-L) shown in the figure, or to the rows/columns, respectively.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Li and Wei submitted A Concise Review of Biomolecule Visualization an indispensable field in the age of next-Generation structure of biomolecule predicted by means of machine learning algorithms. The review is organized in 1) introduction, 2) Visualization Technology, 3) Visualization Tools, 4) Future Challenges and 5) Conclusion. The review is clear and mostly comprehensive.
Below a minor comments about text and figures:
 - Figure 2: the label A to L could be added in the figure legend.
 - lines 82-151: Figure 2A to 2L could be cited within the text
 - lines 105-106: could the authors check the definition of Backbone and Trace models display ?
 - line 117 could the authors clarify "secondary bonds"
 - line 142 could the authors define "OBJ files"
 - table 2 Bioblender is discontinued, it could be added MolecularNodes by Brady A Johnston

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Review of A Concise Review of Biomolecule Visualization by Li & Wei as submitted to Current Issues in Molecular Biology 

Li and Wei provide a readable and interesting high level overview of the current state of biomolecular visualization. Their review briefly surveys from physical models to computational renderings. By taking an agnostic view of the source of information, I think this article will probably be useful for researchers from wide ranges of backgrounds. I think this work should be published, but I do have some questions, comments, and suggestions for the authors. 

Major comments: 

I appreciate the authors mentioning the “cultural factors or personal preference” that might affect color choice and perception on line 199. It would be interesting to develop this a little more, both in terms of currently existing tools and opportunities for better ones. 

The author's discussion of “potential uncertainty of molecular graphics” is interesting. The authors solely mention molecular vibration, but it seems like there is more nuance to the sources of this uncertainty which visualization could help understand. Vibration is obviously an important consideration, but I’d also think a mention of experimental resolution, resonance, and even position-momentum uncertainty introduce ambiguities on the atomic-scale that careful visualization can help resolve. 

The author’s use the perspective of researchers working on the state of the art. However, I often find that innovative visualizations are most useful for students or novices within a field. I wonder if some commentary on the perception from various audiences could be helpful? 

Physical models are mentioned in the context purely as precursors to modern computational visualizations. It seems like 3D printing in the last decade or so has led to a resurgence of physical molecular models. I wonder if these would fit within the scope of this manuscript and if the author’s foresee any opportunities with their use? 

I was greatly intrigued by the author’s passing reference to “Integration of audio” on line 392. I didn’t see an associated reference, but I’d be interested to know more. If there is existing literature, I’d be curious for the author’s to add those references. Even if they don’t have literature in mind, I’d be curious for this idea to be expanded. 

Minor comments: 

In Fig. 2 it would be helpful to include the panel letters in the list of representation models, so names can be matched to the visual more easily. 

“In complex molecular visualization scenarios, when the camera is far from the atoms or when the atoms are scaled down to a volume smaller than one pixel” on line 208. It’s not a camera. I’d recommend rewording somehow. 

What do the authors mean by “Kinetic simulations” on line 242? I’d think dynamics would be more relevant here to atomic uncertainty. The relationship between kinetics and dynamics is subtle, but that subtlety seems relevant in this situation. 

Defining “B-factor” on line 249 would make that section easier to follow.  

Table 2 has some overlapping text between columns. 

What is meant by “interactive path tracing” on line 373? Is this referring to rendering of light rays for perspective? 

Author Response

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Author Response File: Author Response.pdf

Reviewer 4 Report

Referee report on the manuscript entitled: “A Concise Review of Biomolecule Visualization” written by Hui Li and Xinru Wei.

The manuscript submitted for review is a review article on different methods/ways to visualize systems of biological interest. According to the Reviewer opinion the manuscript is well-written and contains valuable information for the scientific community.

The Reviewer has only a few remarks:

The Bibliography of the manuscript is well prepared, however the Authors should format the references in a proper way required by the journal. In addition, concerning some surnames of the authors of the cited papers, the Authors should check and write them correctly (with a proper format of some non-standard letters).

· This helps researchers understand key information, such as atomic structures and bond structures within molecules. – please, rewrite the sentence (explain better), because in the current for it is not clear.

· Figure 2 – in the caption it would be good to add letters describing the representation model.

· It would be appreciated to add a list of abbreviations used in the review article.

· “Table 2 presents a list of commonly used offline molecular visualization software” – maybe it would be better to write software or programs as it is written in Table 2 caption ?

· ProteinShaderGenerates illustrative renderings of proteins – most probably a space is missing. Something happened with the text in Table 2.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

The authors produced a nice review of biomolecular revision and I appreciate their careful replies to my comments and questions. I think this is a valuable summary of the current state of the art and should be published.