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595693085 / DGraphDTA

a novel DTA predition method using graph neural network
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About contact map data files #18

Closed hyojin0912 closed 2 months ago

hyojin0912 commented 11 months ago

Thank you very much for creating a good model and sharing your data. I would like to train the model on proteins other than the ones you used, and I was wondering if you have any contact map data files for other proteins. (Not Kinase, such as GPCR) If I need to create one, I think the running of the alnFilePrepare function needs proteins.txt as input. How do I create a proteins.txt for the proteins I want to experiment with?

595693085 commented 9 months ago

Thanks for you attention on our work. Actually, we provided a script for contact map generation in the code, but it took a long time for it with Pcons4 toolkit. Now, the ems2 model provide a faster and accurate way (a few seconds) for contact map generation on a sequence, and it is easy to implement it (code with three lines). So esm2 (opensouce on github) may solve your problem.