Delineating SARS-CoV-2 spike protein and antibodies interaction interfaces via siamese neural networks: A geometric and image-based analysis
Bibliographic record
Abstract
The analysis of molecular interactions between antigens and antibodies is crucial for understanding the immunological mechanisms underlying the immune response and for developing effective therapies against various diseases. In this context, the ability to distinguish between protein interfaces that form stable and unstable complexes is a key step in the design of therapeutic antibodies and vaccines. In recent years, deep learning models have provided advanced tools for biomedical research. This work introduces a novel approach to analyzing antibody-antigen interactions, and in particular SARS-CoV-2 spike protein-targeting antibodies, using a Siamese Neural Network specifically designed to integrate depth maps with geometric descriptors of molecular surfaces. By combining these representations, the model captures geometrical shape complementarity to differentiate between stable and unstable protein complexes. The network was trained using image-based representations of antigens and antibodies interfaces enriched with geometric descriptors, using data that include binders and non-binders of the SARS-CoV-2 spike protein receptor-binding domain. The deep learning network operates by comparing feature vectors representing these molecular surfaces; pairs with closer vectors in feature space are associated with stable interactions, while those with more distant vectors suggest instability. Extensive testing with different configurations achieved an accuracy of 90%, demonstrating the robustness of this approach to predict interactions. This innovative integration of artificial intelligence, depth maps and geometric descriptors offers promising applications for designing novel antibodies and vaccines.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".