Is There a Need for a More Precise Description of Biomolecule Interactions to Understand Cell Function?

Round 1

Reviewer 1 Report

• Author need to modify the title to make it easy for reader, For example, you can start from examination of .....
• The orginzation of the manuscipt should be modified. Make the short title for each sub-section.
• Figure 1 needs more desciption
• Please add one table for section Current state of interactome databases to show all database used and their pros and cons. Public or private dataset.
• You can add table or analysis for discussion section.
• The literature review needs to update based on recent related works
• https://doi.org/10.1016/j.jbi.2020.103627
•  Genes 2021, 12(2), 186; https://doi.org/10.3390/genes12020186
• DOI: 10.3934/mbe.2021440

Author Response

Reviewer 1

Comments and suggestions for authors

The author thanks the reviewer for his reading of the manuscript and suggestions.

 

Author need to modify the title to make it easy for reader, For example, you can start from examination of .....

We thought that the title recapitulated well the purpose of the paper. However, we agree that it is important to make the reader's task as easy as possible. Therefore, the title was completed with a few words and the abstract was thoroughly rewritten to make the purpose of the paper easier to grasp for the reader.

 

The orginzation of the manuscipt should be modified. Make the short title for each sub-section.

It is not clear to the author why the organization of the manuscript should be modified. It was checked that each section and each sub-section had a short title and this short title was made as clear as possible.

 

Figure 1 needs more desciption

Two references were added in the legend of figure 1. However, this was viewed as a simple example that should be easily understood.

 

Please add one table for section Current state of interactome databases to show all database used and their pros and cons. Public or private dataset.

It would be impossible to describe available databases (as indicated in ref. 130 of the revised paper "As of December 2011, the PathGuide resource 1 listed more than 100 protein-protein interaction–related data-bases"). We added Table 1 to illustrate the qualitative nature of information immediately retrieved with several representative databases. We included only public databases since the author is convinced that scientific information should be freely available. This is the reason why he was glad to submit this paper to CIMB, an open journal.

 

You can add table or analysis for discussion section.

The last section was entirely rewritten to emphasize what were considered as the main points of the paper.

 

 

The literature review needs to update based on recent related works

https://doi.org/10.1016/j.jbi.2020.103627

 Genes 2021, 12(2), 186; https://doi.org/10.3390/genes12020186

DOI: 10.3934/mbe.2021440

While both references suggested by the referee are interesting, it must be pointed out that it was quite impossible to quote even a small fraction of published material [a PubMed query with "(deep learning) OR (artificial intelligence) OR (systems biology)" retrieved 337,909 papers, including 57,446 reviews !] and the "large amount of literature cited" (as acknowledged by the second reviewer) was selected in view of the authors preferences as well as relevance to the interactome. However, we were glad to add the paper that appeared in Genes, since it was found to fit in the review (see §2.3).

 

Author Response File: Author Response.pdf

Reviewer 2 Report

The author of the work entitled: Is there a need for a more precise description of biomolecule interactions? tries to introduce the reader to data processing methods such as computer simulation, deep learning, logical representation or network analysis. It is suggested that more loosely defined properties such as conformational flexibility or binding molecule size could include important information.

In my opinion, this review does not bring anything interesting to the reader on this topic. The manuscript is very badly written. There is no substantive justification of the topic, despite the large amount of literature cited.

The very summary of the author raises doubts as to the content presented:

While it was obviously not feasible to bring a clear-cut answer to this question in this review, it was felt useful to try and present pieces of information that might serve as a minimal basis to address this problem.

Author Response

Reviewer 2

Comments and Suggestions for Authors

The author of the work entitled: Is there a need for a more precise description of biomolecule interactions? tries to introduce the reader to data processing methods such as computer simulation, deep learning, logical representation or network analysis. It is suggested that more loosely defined properties such as conformational flexibility or binding molecule size could include important information.

The author thanks the reviewer for reading the manuscript, and he is happy that he did not point out any error or ambiguity in the description of data processing methods ; however (see answer to reviewer 1 and revised abstract) the purpose of the paper was only to emphasize an question that was deemed important by the author, and the description of data processing methods was only intended to emphasize the importance of the choice of parameters. We agree that this might not be clear enough, and the abstract and conclusion section were entirely rewritten.

In my opinion, this review does not bring anything interesting to the reader on this topic.

The author think that the interest of the review should be assessed on the basis of the following points : (i) Is the question emphasized in the title important ? (ii) Is it warranted to examine this question, or is the answer obvious to investigators ? (iii) is the material collected in the review relevant to the studied problem ? (iv) is the collected material useful, or should it be considered as trivial by all members of the scientific community ? The review was build by keeping these questions in mind, and bearing on the opinion of many colleagues that felt that papers currently appearing in highly respected journals (such as Cell) are more and more difficult to fathom.

The manuscript is very badly written. There is no substantive justification of the topic, despite the large amount of literature cited.

The author would have been grateful to the reviewer if he had explained more clearly why he felt that the manuscript was very badly written.

The very summary of the author raises doubts as to the content presented:

While it was obviously not feasible to bring a clear-cut answer to this question in this review, it was felt useful to try and present pieces of information that might serve as a minimal basis to address this problem.

The author agrees that the summary was not clear enough, and the last section was completely rewritten. What he meant in the above sentence is that he would have been overconfident if he had provided a clearcut list of parameters that should be incorporated into interactome databases, and he only gave some specific examples (selected according to his own experience and interest) to convince the reader that the question raised in the review was not settled, and was indeed very difficult to answer.

 

Author Response File: Author Response.pdf

Reviewer 3 Report

I was pleased to read your review, very specific lecture and a well organized structure, a small comment I could do on the simplicity of the way you explain the figures. 

I accept the review in this form

Author Response

The author thanks the reviewer for his positive comment. The manuscript was carefully reread and a few typographical errors were corrected. Figures were improved and some information was added in figure legends