Theoretical and Natural Science
- The Open Access Proceedings Series for Conferences
Vol. 15, 04 December 2023
* Author to whom correspondence should be addressed.
HER2 is a crucial marker in cancer diagnosis and targeted treatment. Accurate structure prediction and analysis of HER2 are vital for understanding its function and designing effective therapies. Our study proposes an end-to-end and artificial intelligence approach that uses deep learning frameworks to predict and analyze HER2’s structure. Using top-notch machine learning algorithms, we trained a model on a comprehensive dataset of HER2 sequences and structures. The model showed impressive accuracy in forecasting HER2’s tertiary structure, helping identify potential functional areas and critical interaction points. Moreover, our analysis provided new insights into HER2’s structural changes and stability, revealing potential regulation mechanisms for targeted therapies. We used advanced bioinformatics tools to validate our predictions and ensure their reliability. This research marks a significant step in understanding HER2’s molecular structure and lays a solid groundwork for personalized cancer treatments. By harnessing artificial intelligence, our study offers a promising path for precise medicine and targeted treatments for HER2-overexpressing cancers.
Alphafold2, Protein Structure Prediction, Deep Learning, HER2
1. Jumper J, Evans R, Pritzel A. et al. 2021 Highly accurate protein structure prediction with AlphaFold. Nature 596 583–589
2. Mullard A 2021 What does AlphaFold mean for drug discovery? Nature reviews. Drug Discovery 20 725-727
3. Ishikawa T, Seto M, Banno H et al. 2011 Design and synthesis of novel human epidermal growth factor receptor 2 (HER2)/epidermal growth factor receptor (EGFR) dual inhibitors bearing a pyrrolo[3,2-d]pyrimidine scaffold. J Med Chem 54 8030–8050
4. Erdo F, Gordon J, Wu J T, Sziraki I 2012 Verification of brain penetration of the unbound fraction of a novel HER2/EGFR dual kinase inhibitor (TAK-285) by microdialysis in rats. Brain Res Bull 87 413–419
5. https://www.rcsb.org
6. Moult J, Fidelis K, Kryshtafovych A, Schwede T and Topf M 2020 Critical assessment of techniques for protein structure prediction, fourteenth round. CASP 14 Abstract Book https://www.predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf
7. https://colab.research.google.com
8. https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
9. Robertson A, Courtney J, Shen Y, et al. 2021 Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society 143 19306-19310
10. Callaway E 2021 DeepMind’s AI predicts structures for a vast trove of proteins. Nature 595 635
11. https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1
12. Ren F, Ding X, Zheng M, et al. 2022 Alphafold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel cyclin-dependent kinase 20 (CDK20) small molecule inhibitor. arXiv e-prints.
The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.
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