Reviewer name and names of any other individual's who aided in reviewer	Prashanth N Suravajhala
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?	Yes
Additional Comments	The authors could describe Minimum Information about bioinformatics investigation (MIABI) guidelines
Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code?	Yes
Additional Comments	github and Zenodo, yes! I tested git, forked it and as I didn't test the graphical version, ensured all python libraries are working!
As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
Additional Comments	Yes, please
Is the code executable?	Yes
Additional Comments
Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
Additional Comments
Is the documentation provided clear and user friendly?	Yes
Additional Comments	Yes, a white paper could be more friendly!
Is there enough clear information in the documentation to install, run and test this tool, including information on where to seek help if required?	Yes
Additional Comments
Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
Additional Comments	yes with README version!
Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Yes
Additional Comments	Yes, as described by the authors
Is test data available, either included with the submission or openly available via cited third party sources (e.g. accession numbers, data DOIs)?	No
Additional Comments
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments	The Molecular Property Dynamic Suite (MPDS) is a welcome initiative which would serve chemical space for research community. While the authors aimed to deploy it in Galaxy, there is no Galaxy reference cited in first few introductory lines. A strong rationale on Galaxy-MPDS connect could be a value addition The port 8085/8080 are ephemeral and it would be nice if the authors deploy it on a more permanent base An absolute strength for the suite is availability of source code so that end-users can fine tune and reinstantiate the codes. In the architecture, could the end user have a chance to deploy biopython modules for drug discovery/modeling In Page 4, the authors can define what are the tools precisely used in MPDS 2.3 section: The PPI is not abbreviated as first use The results are exploited well for disease dependent/independent use. However, the major challenge for ligand use/preparation is the use of ncRNAs. Could MPDS provide such instances where ncRNAs could be used fpr targeted ligands? L28 in section 4.1: Pluralis for features ( as one of is used) Also a word or two on aadhar card for perhaps naive users may be mentioned and it may be italicized as it may be a domestic word. Does MPDS suite augur well for Anvaya that Government of India launched, or Tavexa or Taverna? A word to two on local setting up of cloud instance may be a nice addition Scores on a scale of 0-5 with 5 being the best Language: 4 Novelty: 4.5 Brevity: 4 Scope and relevance: 4
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
Additional Comments	Language/Brevity checks: Page 9 L6: fulfill misspelt webserver are two words, IMHO Page 10: CADD which IS available Tabl S2/S4: from THE coronavirdiae space between anticoronavirusdrugs Figure S3: remove OF (identifying OF existing) Supporting information may be corrected
Any Additional Overall Comments to the Author	High resolution Figures esp GA, Figures 2-4 may be inserted
Recommendation	Minor Revisions