Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features
Abstract
1. Introduction
2. Materials and Methods
2.1. Dataset
2.2. Definition of Interface Residues
2.3. Multiple Sequence Alignment Extraction
2.4. Sequence-Based Features
2.4.1. Extracting Coevolutionary Features
2.4.2. TM Monomer Sequence Motifs
2.4.3. LIPS Scores
2.4.4. Structure-Based Features
3. Results
3.1. Comparing TM Proteins Surface-Based vs. Attention-Based Models
3.1.1. Extracting the Predicted Structures
3.1.2. Extracting Interface Residues
3.1.3. PREDDIMER Outperforms RoseTTAFold2 and AlphaFold2Multimer
3.2. TMH-ID Model
3.2.1. Comparing TMH-ID to ProteinBert, MSA Transformer, and THOIPA
3.2.2. Comparing TMH-ID to PREDDIMER, AlphaFold2Multimer, and RoseTTAFold2
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Model | Mean Precision | Mean Recall | Mean F1 Score |
---|---|---|---|
RoseTTAFold2 | |||
AlphaFold2Multimer | |||
PREDDIMER |
Model | Mean Precision | Mean Recall | Mean F1 Score |
---|---|---|---|
THOIPA | |||
ProteinBert | |||
MSA-Transformer | |||
TMH-ID (ours) |
Model | Mean Precision | Mean Recall | Mean F1 Score |
---|---|---|---|
RoseTTAFold2 | |||
AlphaFold2Multimer | |||
PREDDIMER | |||
TMH-ID |
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Almalki, B.; Liao, L. Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features. Int. J. Mol. Sci. 2025, 26, 4270. https://doi.org/10.3390/ijms26094270
Almalki B, Liao L. Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features. International Journal of Molecular Sciences. 2025; 26(9):4270. https://doi.org/10.3390/ijms26094270
Chicago/Turabian StyleAlmalki, Bander, and Li Liao. 2025. "Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features" International Journal of Molecular Sciences 26, no. 9: 4270. https://doi.org/10.3390/ijms26094270
APA StyleAlmalki, B., & Liao, L. (2025). Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features. International Journal of Molecular Sciences, 26(9), 4270. https://doi.org/10.3390/ijms26094270