I agree with gaborous in that you maybe seeking standardization, and a quick search for a visualization reveals lectures on why standardization is useful.

TLDW version is that this is all to avoid squashed (elliptical or canoe) shaped input space, because such shapes will cause linear regression to wander.

Credit to Blitz Kim

Now from what little I've grokked of the fields concerned it seems as though one can get away with ranges that do not produce a nice dartboard like shapes, eg -1 to 1 and 0 to 3, however, ranges greater than 1 or less than -1 may cause high variability in outputs, or lead to the exploding or vanishing gradient problem.

Supposedly there are activation functions and other methods that can be used that are more resilient or less likely to be susceptible to gradients misbehaving, but when a little data massaging can mitigate having a latter fight with debugging a model, it seems like a far better choice to pre-clean the input space.

As to what makes sense or not... personally when reading (and re-reading) the question my instinct would be to suggest adapting something like word2vec for the data to input encoding method and feeding that to a GCN for classification and perhaps generation. Because supposedly word to vector methods better preserve relationships (like similar meanings of words) between data, and Graph Convolution Networks supposedly do really well at point cloud inputs, which is kinda what word2vec methods output... But this is just based off speculation on what it is that you're attempting to do, and what I've learned on these subjects.

I agree with gaborous in that you maybe seeking standardization, and a quick search for a visualization reveals lectures on why standardization is useful.

TLDW version is that this is all to avoid squashed (elliptical or canoe) shaped input space, because such shapes will cause linear regression to wander.

Credit to Blitz Kim

Now from what little I've grokked of the fields concerned it seems as though one can get away with ranges that do not produce a nice dartboard like shapes, eg -1 to 1 and 0 to 3, however, ranges greater than 1 or less than -1 may cause high variability in outputs, or lead to the exploding or vanishing gradient problem.

Supposedly there are activation functions and other methods that can be used that are more resilient or less likely to be susceptible to gradients misbehaving, but when a little data massaging can mitigate having a later fight with debugging a model, it seems like a far better choice to pre-clean the input space.

As to what makes sense or not... personally when reading (and re-reading) the question my instinct would be to suggest adapting something like word2vec for the data to input encoding method and feeding that to a GCN for classification and perhaps generation. 

Because supposedly word to vector methods better preserve relationships, like similar meanings of words, or perhaps in this case similar functions between proteins that may seem unrelated at first glance in structure. And Graph Convolution Networks, because supposedly they do really well at point cloud inputs, which is kinda what word2vec methods output 

But this is just based off speculation on what it is that you're attempting to do, and what I've learned on these subjects. Essentially I'd treat proteins as paragraphs because they express that level of complex meaning/intent.