User:Zachbergevin/Protein-ligand docking/Aspezikian Peer Review

Whose work are you reviewing?

 * Zach-@zachbergevin
 * Link to draft you're reviewing Protein–ligand docking

Link to previous draft
https://en.wikipedia.org/w/index.php?title=Protein%E2%80%93ligand_docking&oldid=1036200432

Evaluate the drafted changes
Hi Zach! Here's my peer review for you,

Lead


 * 1) Has the Lead been updated to reflect the new content added by your peer? A new lead has been fully edited. However, it may be an area that requires more focus on editing.
 * 2) For example, I recommend creating a new paragraph on this in the Lead and adding the previous sentence in the original article on docking applications and software- "There has been rapid development in computational ability to determine protein structure with programs such as AlphaFold, and the demand for the corresponding protein-ligand docking predictions is driving implementation of software that can find accurate models. "
 * 3) add this sentence in new paragraph and rephrase it to introduce ideas better- "Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide."
 * 4) delete this sentence in Lead and/or maybe add it in "purpose or future" section- "Once the protein folding can be predicted accurately along with how the ligands of various structures will bind to the protein, the ability for drug development to progress at a much faster rate becomes possible."
 * 5) Does the Lead include an introductory sentence that concisely and clearly describes the article's topic? Yes, the introduction sentence is very clear, and i do not recommend editing it.
 * 6) Does the Lead include a brief description of the article's major sections? No, I recommend adding a couple sentences on examples of available software (please see above comments), when it was first created (like a sentence), and introduce idea of protein flexibility and applications in relevant paragraph in the Lead.
 * 7) Does the Lead include information that is not present in the article? Not really, only briefly was future implications was included in the Lead. I recommend adding a "future implication" section would be great if possible in this article.
 * 8) " Once the protein folding can be predicted accurately along with how the ligands of various structures will bind to the protein, the ability for drug development to progress at a much faster rate becomes possible."
 * 9) Is the Lead concise or is it overly detailed? The Lead is concise, but it does require edits in sentence phrasing and paragraph restructuring and include relevant information above in order to clearly bring up information shown in the other parts of the article.

Content


 * 1) Is the content added relevant to the topic? Yes, expanding the protein flexibility and available software sections with new citations in the article is very relevant. I recommend adding more sections on background and other current research and applications of this technology. I think you need to expand on the different types of each software. I think you also need to organize more sub-sections within a header to be more clear on the flow of information.
 * 2) Is the content added up-to-date? - Yes many of the articles you've added into the article are fairly new (from the 2000's). However, I do see that you did not cite your content within the article, which is key.
 * 3) Is there content that is missing or content that does not belong? -Yes, i think a section of history and background of this technology is necessary. I also think adding more citations within article is critical. I recommend also focusing on new research advances and other applications. It would also be interesting to see a section on methods and evaluation of this technology. I recommend trying to using the Macromolecular docking article as reference to how to expand and organize your article.
 * 4) Does the article deal with one of Wikipedia's equity gaps? Does it address topics related to historically underrepresented populations or topics? - Yes, it addresses molecular docking, which is a fairly new biotech development. I think addressing its future implications in pharmacology more clearly and in depth in a new section would make this article more thorough.

Tone and Balance


 * 1) Is the content added neutral? - yes, for the most part, I see no signs of tone, which is integral in a biotechnology articles. However, this sentence may seem not neutral if included in the Lead- "Once the protein folding can be predicted accurately along with how the ligands of various structures will bind to the protein, the ability for drug development to progress at a much faster rate becomes possible." I recommend creating a section of "future implications" to discuss this or only rephrasing this sentence and adding a citation.
 * 2) Does the content added attempt to persuade the reader in favor of one position or away from another? Not at all. Great job in keeping article informative and neutral
 * 3) Are there viewpoints that are overrepresented, or underrepresented?-I think a viewpoint on future implications is missing, which was only talked about briefly in the Lead.

Sources and References


 * 1) Is all new content backed up by a reliable secondary source of information? - Yes, most new content is backed up by a reliable secondary source. I recommend gathering more and citing more content from research publications and journals. I definitely think you need to cite your articles more in your wiki page.
 * 2) Are the sources thorough - i.e. Do they reflect the available literature on the topic? - Sources are thorough! Great job!
 * 3) Are the sources current? - Yes, many of the articles you've added into the article are fairly new (from the 2000's).
 * 4) Are the sources written by a diverse spectrum of authors? Do they include historically marginalized individuals where possible? - I dont think this is a concern since this is a biotechnology article.
 * 5) Are there better sources available, such as peer-reviewed articles in place of news coverage or random websites? (You may need to do some digging to answer this.) - I do see many use of peer-reviewed articles. I think you need to look into and cite more peer-reviewed articiles and journals. I recommend after gathering more peer-reviewed articles, maybe use cited resources from those articles to find more relevant information in order to expand your article.

Organization


 * 1) Is the content added well-written - i.e. Is it concise, clear, and easy to read? Yes, it easy to read. I think some sentence rephrasing and paragraph restructuring is needed for the Lead and sections.
 * 2) make new paragraph or sub-section-"Root Mean Square Deviation is the standard method of evaluating various software performance within the binding mode of the protein-ligand structure. Specifically, it is the root-mean-squared deviation between the software-predicted docking pose of the ligand and the experimental binding mode. The RMSD measurement is computed for all of the computer-generated poses of the possible bindings between the protein and ligand. The program does not always perfectly predict the actual physical pose when evaluating the RMSD between candidates. In order to then evaluate the strength of a computer algorithm to predict protein docking, the ranking of RMSD among computer-generated candidates must be examined to determine whether the experimental pose actually was generated but not selected."
 * 3) Does the content added have any grammatical or spelling errors? Here are some segments that I think could use fixing, just my suggestions:
 * 4) -comma after "and"--- "Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide."
 * 5) -rephrase, does not flow, why past tense?: "In particular, one such program used to model peptides as the specific ligand bonding to the protein is DockThor"
 * -: use "have"- " Peptides are a highly flexible type of ligand that has proven to be a difficult type of structure to predict in protein bonding programs..”
 * 1) - put (RSMD) next to this- " Root Mean Square Deviation"
 * 2) why passsive? write "computes"--"The RMSD measurement is computed for all of the computer-generated poses of the possible bindings between the protein and ligand. "
 * 3) rephase like "Thus, in order to evaluate..."---" In order to then evaluate the strength of a computer algorithm to predict protein docking, the ranking of RMSD among computer-generated candidates must be examined to determine whether the experimental pose actually was generated but not selected."
 * 4) rephrase" However, dealing with receptor flexibility in docking methodologies is still a thorny issue."
 * 5) Is the content added well-organized - i.e. broken down into sections that reflect the major points of the topic? - Yes, it's broken down into sections/general headings and then with specific details. I recommend using subheaders in the "available software" and "protein flexibility" section when adding more relevant information. Maybe look into adding more sections in your article like including history of protein-ligand docking and relevant research and technologies. I think you can expand on the "available software" section by creating a subsection for each software and writing a brief paragraph about it. I also recommend creating a sub section of "AutoDocs" in the "protein flexibility section. Overall, I think you need to expand on the topics background, research advancements, technologies, and etc if possible.

Overall impressions


 * 1) Has the content added improved the overall quality of the article - i.e. Is the article more complete?/How can the content added be improved? - Yes, content added highly imporved overall quality of article and it is "more complete". I think you need to expand on the topics background, research advancements, technologies, and etc if possible, but I understand that could be difficult since it is a new technology. Maybe expand on available software and the general purposes of protein-ligand docking?
 * 2) What are the strengths of the content added? Adding the "available software" and "protein flexibility"section was really key. Clarity and appropraite amounts of details makes this article highly informative and highly understandable. Good job :)

Additional Questions


 * Does your peer have 5-7 reliable sources? You have 6 sources so far which is great! I recommend looking for and citing more peer-reviewed articles and publications.
 * Does the topic link in some way to our course material? Definitely, It is really awesome to see applications of biotechnology within screening.
 * Does your peer add historical context to their article? No, I highly recommend adding a section on the history of development of protein-ligand docking. I think this would improve the quality of the article.
 * Based on what you know from course content, what do you think Wikipedia users should know about this topic? In other words, what would you recommend adding and/or considering further? As said before, I think expanding, creating new subheaders, and citing sources in article is key in advancing this topic.

-Ashley