Open Peer-Review

Provide the website of the platform. Because when I tried to look it up, there are quite some website with similar name.

If you use Generative AI for the development of this manuscript, in any instances of the section, you should declare it in the acknowledgement. The declaration could be something like this " The MARA AI was deployed for improving the [SECTIONS] of the manuscript". You need to explain in more detail in the acknowledgement, what aspect of the manuscript that developed by the agent.

The methodology section is not detailed enough. You should explain how you retrieve the data, what PDB ID you use, what PUBCHEM ID for your ligand, how are you going to validate your docking method (with a standard drug, or with a decoy).

Moreover, you should explain your PASS server Pa cut off

No online generative AI bypass the HPC infrastructure, because they are using it anyway. It just relieve the need to use HPC in the end user side, not the server side.

Can MARA AI help you to do MD? If it can do it, better you do the MD as well

Can you ask the MARA AI to provide all the python and shell script deployed in this project? If they can't provide it, it is a concerning limitation as well. Because it is impossible to replicate the simulation. On the other hand, standard generative AI platform such as Claude and Codex could provide the source code, so replication is easy. You should discuss this in the study limitation.

In bioinformatics, if you can't access the source code, it is not democratic at all. Better rephrase this wording into something else, such as "make it easier" or else.