search

BernhoferM / TMbed

Transmembrane proteins predicted through Language Model embeddings
Apache License 2.0
30 stars 3 forks source link

using language model (ESM) to predict transmembrane proteins #1

Closed wangleiofficial closed 2 years ago

wangleiofficial commented 2 years ago

hello, Michael Bernhofer DeepTMpred (https://www.sciencedirect.com/science/article/pii/S2001037022001428) should be the first tool to use a language model (ESM) to predict transmembrane proteins, if possible, you can add this method to the comparison, thank you very much!

BernhoferM commented 2 years ago

Dear Lei Wang, Unfortunately, we have not been aware of your method when working on the manuscript. Since the manuscript has already been accepted and published, we cannot add your method to our comparisons anymore. However, we have not claimed to be the first method to use pLMs for transmembrane protein prediction (if that is your concern). In fact, we specifically refer to DeepTMHMM (pre-print: https://doi.org/10.1101/2022.04.08.487609), another method that uses a pLM (ESM-1b).

Regards Michael Bernhofer

wangleiofficial commented 2 years ago

@BernhoferM Congratulations that your manuscript has been accepted, your tool has been compared to DeepTMHMM, but its paper is also later than DeepTMpred. If possible, you can add an introduction of DeepTMpred to the preprint paper, thanks again!

BernhoferM commented 2 years ago

The bioRxiv preprint cannot be changed either. Their FAQ states: "An article posted on bioRxiv can be revised at any time, until it is accepted for publication." Since it has been accepted and published, the preprint should not be changed.

Regards Michael Bernhofer