Predicting Transmembrane Protein Topology from 3D Structure

[Submitted on 24 Sep 2026]

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Abstract:This paper presents a novel approach to infer protein topology using the state-of-the-art graph neural network (GNN), SchNet. The model is trained on the same dataset used to develop the recent DeepTMHMM model with 5-fold cross-validation. Unlike the conventional approaches based on using only the protein sequences or the $\alpha$-carbons as features, we have decoded our classifier in this way, so all atom-level embeddings are used. Without applying any pre-trained weight, the final results have shown great potential that GNNs can be used for topological predictions.

Submission history

From: Xiaopeng Mao [view email]
[v1] Thu, 24 Sep 2026 18:38:33 UTC (3,727 KB)