Protein structure prediction based on deep learning: HER2 in complex with a covalent inhibitor

Wenyi Yao

doi:10.54254/2977-3903/6/2024056

Article Information

Received: 20 February 2024

Published: 20 February 2024

DOI: https://doi.org/10.54254/2977-3903/6/2024056

Article Type: Research Article

Cite this article

Yao,W. (2024). Protein structure prediction based on deep learning: HER2 in complex with a covalent inhibitor. Advances in Engineering Innovation,6,13-20.

Data availability

The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.

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About this Volume

Volume Title: AEI Vol.6

Part of Series: Advances in Engineering Innovation

ISSN: 2977-3903 (Print) / 2977-3911 (Online)

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[1]O’Connor C M, Adams J U and Fairman J E 2010 Essentials of Cell Biology (Cambridge, MA: NPG Education)

[2]Branden C I and Tooze J 2012 Introduction to Protein Structure, second edition (Boca Raton, FL: Garland Science)

[3]Al-Lazikani B, Jung J, Xiang Z and Honig B 2001 Protein structure prediction Curr. Opin. Chem. Biol. 5 51–6

[4]Kryshtafovych A, Schwede T, Topf M, Fidelis K and Moult J 2021 Critical assessment of methods of protein structure prediction (casp)—round xiv Proteins 89 1607–17

[5]Jumper J et al. 2021 Highly accurate protein structure prediction with alphafold Nature 596 583–9

[6]Gao M, Nakajima An D, Parks J M and Skolnick J 2022 Af2complex predicts direct physical interactions in multimeric proteins with deep learning Nat. Commun. 13 1744

[7]Linger R M, Keating A K, Earp H S and Graham D K 2008 TAM Receptor Tyrosine Kinases: Biologic Functions, Signaling, and Potential Therapeutic Targeting in Human Cancer Adv. Cancer Res. 100 35–83

[8]Hynes N E and MacDonald G 2009 ErbB receptors and signaling pathways in cancer Curr. Opin. Cell Biol. 21 177–84

[9]Graus-Porta D 1997 ErbB-2, the preferred heterodimerization partner of all ErbB receptors, is a mediator of lateral signaling EMBO J. 16 1647–55

[10]Yarden Y 2001 Biology of her2 and its importance in breast cancer Oncology, suppl.S2 61 1–13

[11]Wilding B et al. 2022 Discovery of potent and selective her2 inhibitors with efficacy against her2 exon 20 insertion-driven tumors, which preserve wild-type egfr signaling Nat. Cancer 3 pp. 821–36

[12]Berman H M 2000 The protein data bank Nucleic Acids Res. 28 pp. 235–42

[13]Bader G 2022 Her2 in complex with a covalent inhibitor wwPDB

[14]Schrödinger, LLC 2015 The PyMOL molecular graphics system, version 1.8

[15]Adasme M F, Linnemann K L, Bolz S N, Kaiser F, Salentin S, Haupt V, and Schroeder M 2021 Plip 2021: expanding the scope of the protein–ligand interaction profiler to dna and rna Nucleic Acids Res. 49 W530–4