[Submitted on 24 Sep 2026]
Title:Predicting Transmembrane Protein Topology from 3D Structure
View a PDF of the paper titled Predicting Transmembrane Protein Topology from 3D Structure, by Sitong Chen and 1 other authors
View PDF HTML (experimental)
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.
Subjects:
Artificial Intelligence (cs.AI)
Cite as: arXiv:2609.30446 [cs.AI]
(or arXiv:2609.30446v1 [cs.AI] for this version)
https://doi.org/10.48550/arXiv.2609.30446
arXiv-issued DOI via DataCite (pending registration)
Submission history
From: Xiaopeng Mao [view email] [v1] Thu, 24 Sep 2026 18:38:33 UTC (3,727 KB)
Full-text links:
Access Paper:
View a PDF of the paper titled Predicting Transmembrane Protein Topology from 3D Structure, by Sitong Chen and 1 other authors
View PDF
HTML (experimental)
TeX Source
view license
Current browse context:
cs.AI
new | recent | 2026-09
Change to browse by:
cs
References & Citations
NASA ADS
Google Scholar
Semantic Scholar
Loading...
Data provided by:
Bibliographic Tools
Bibliographic and Citation Tools
Bibliographic Explorer Toggle
Bibliographic Explorer (What is the Explorer?)
Connected Papers Toggle
Connected Papers (What is Connected Papers?)
Litmaps Toggle
Litmaps (What is Litmaps?)
scite.ai Toggle
scite Smart Citations (What are Smart Citations?)
Code, Data, Media
Code, Data and Media Associated with this Article
alphaXiv Toggle
alphaXiv (What is alphaXiv?)
Links to Code Toggle
CatalyzeX Code Finder for Papers (What is CatalyzeX?)
DagsHub Toggle
DagsHub (What is DagsHub?)
GotitPub Toggle
Gotit.pub (What is GotitPub?)
Huggingface Toggle
Hugging Face (What is Huggingface?)
ScienceCast Toggle
ScienceCast (What is ScienceCast?)
Demos
Demos
Replicate Toggle
Replicate (What is Replicate?)
Spaces Toggle
Hugging Face Spaces (What is Spaces?)
Spaces Toggle
TXYZ.AI (What is TXYZ.AI?)
Related Papers
Recommenders and Search Tools
Link to Influence Flower
Influence Flower (What are Influence Flowers?)
Core recommender toggle
CORE Recommender (What is CORE?)
Author
Venue
Institution
Topic
About arXivLabs
arXivLabs: experimental projects with community collaborators
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.
Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.
Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)