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ProtRAP-LM: Efficient Protein Relative Accessibility Prediction and Proteome-wide Membrane Protein Screening
Lei Wang1,2, Kai Kang1,2, Chen Song1,2
1Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
Genomics, Proteomics & Bioinformatics
|February 15, 2026
Summary
A new model, ProtRAP-LM, uses protein language models to quickly predict membrane protein properties. This tool accelerates the analysis of membrane proteins across entire proteomes, aiding future research into their structure and function.
Area of Science:
- Biochemistry
- Computational Biology
- Structural Biology
Background:
- Membrane proteins are crucial for cellular functions and are key therapeutic targets.
- Accurate prediction of membrane protein properties is essential for drug discovery and biological research.
- Previous methods relied on multiple sequence alignments (MSAs), limiting prediction speed.
Purpose of the Study:
- To develop a rapid and accurate method for predicting membrane protein properties.
- To leverage protein language models (pLMs) for enhanced prediction capabilities.
- To overcome the speed limitations of MSA-based prediction models.
Main Methods:
- Introduced ProtRAP-LM, a transformer-based model utilizing pLM embeddings.
- Applied the model to predict membrane contact probability (MCP) and residue relative accessibility.
- Evaluated performance on a 184-protein test set.
Main Results:
- ProtRAP-LM achieved superior performance compared to previous MSA-based models.
- Demonstrated a speed-up of over 300 times, enabling proteome-wide predictions within hours.
- Provided comprehensive annotations for challenging membrane protein types, including single-pass transmembrane and beta-sheet proteins.
Conclusions:
- ProtRAP-LM offers a significant advancement in the rapid and accurate prediction of membrane protein properties.
- Facilitates large-scale proteome annotations, providing a valuable resource for biological research.
- Enables deeper investigation into the structure and function of essential membrane biomolecules.
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