Delineating SARS-CoV-2 spike protein and antibodies interaction interfaces via siamese neural networks: A geometric and image-based analysis
Gemma Loreti, Paola Vottero, Elena Carlotta Olivetti, Enrico Vezzetti, Jack Tuszynski, Federica Marcolin, Maral Aminpour
TL;DR
This paper uses a deep learning model to analyze how antibodies interact with the SARS-CoV-2 spike protein, helping design better vaccines and therapies.
Contribution
A novel Siamese Neural Network integrating depth maps and geometric descriptors to predict stable antibody-antigen interactions.
Findings
The model achieved 90% accuracy in predicting stable versus unstable antibody-antigen interactions.
Combining depth maps and geometric descriptors improves the ability to detect shape complementarity in molecular interfaces.
The approach is robust and applicable to designing new antibodies and vaccines.
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…
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Taxonomy
Topicsvaccines and immunoinformatics approaches · Computational Drug Discovery Methods · SARS-CoV-2 and COVID-19 Research