I'm an undergraduate biology student and my thesis is on designing a deep learning architecture to predict whether two proteins interact or not given their primary sequences. I have read some papers with different approaches to the problem including the paper [https://academic.oup.com/bioinformatics/article/35/14/i305/5529260] uses PIPR model which is the state of the art model for this problem in 2019 and recently in 2021 the paper [https://www.biorxiv.org/content/10.1101/2021.01.22.427866v1] uses D-SCRIPT which surpass PIPR with the aspect of the small dataset and has better generalization feature for many model organisms.

For my problem, I have two questions

  1. can you suggest to me the approach to build a model for my thesis. Should I follow these papers to build a model, how my model will be different from the models in the papers?
  2. Which architecture or model recently that the literature considers the most proper for the protein-protein interaction prediction approach?

I very much appreciate any help from everyone!

  • $\begingroup$ Albeit to make a full structure... Check out github.com/sokrypton/ColabFold it's a mod of the AlphaFold2 notebook. Albeit not mentioned by AlphaFold2, the Rosettafold paper talks about complexes. It's not benchmarked. If two proteins don't interact the replicates will differ. $\endgroup$ Aug 22 '21 at 6:56
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    $\begingroup$ I’m voting to close this question because it is opinion-based and not on-topic. Thesis guidance should be done by a local supervisor, not by strangers on the internet. This has also been asked over at biostars.org (but I cannot find the link) where an experienced member added a good response poiting out that the aim of this endeavour seems to go way beyond of what an undergraduate can/should do. $\endgroup$
    – ATpoint
    Sep 2 '21 at 8:52
  • $\begingroup$ Here is the post mentioned by @ATPoint: biostars.org/p/9485815 $\endgroup$
    – Ram RS
    Sep 2 '21 at 15:54

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