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Learned protein embeddings for machine learning.
Yang KK, Wu Z, Bedbrook CN, Arnold FH. Yang KK, et al. Among authors: wu z. Bioinformatics. 2018 Aug 1;34(15):2642-2648. doi: 10.1093/bioinformatics/bty178. Bioinformatics. 2018. PMID: 29584811 Free PMC article.
Learned protein embeddings for machine learning.
Yang KK, Wu Z, Bedbrook CN, Arnold FH. Yang KK, et al. Among authors: wu z. Bioinformatics. 2018 Dec 1;34(23):4138. doi: 10.1093/bioinformatics/bty455. Bioinformatics. 2018. PMID: 29933431 Free PMC article. No abstract available.
Signal Peptides Generated by Attention-Based Neural Networks.
Wu Z, Yang KK, Liszka MJ, Lee A, Batzilla A, Wernick D, Weiner DP, Arnold FH. Wu Z, et al. ACS Synth Biol. 2020 Aug 21;9(8):2154-2161. doi: 10.1021/acssynbio.0c00219. Epub 2020 Jul 27. ACS Synth Biol. 2020. PMID: 32649182 Free article.
Advances in machine learning for directed evolution.
Wittmann BJ, Johnston KE, Wu Z, Arnold FH. Wittmann BJ, et al. Among authors: wu z. Curr Opin Struct Biol. 2021 Aug;69:11-18. doi: 10.1016/j.sbi.2021.01.008. Epub 2021 Feb 26. Curr Opin Struct Biol. 2021. PMID: 33647531 Review.
Protein sequence design with deep generative models.
Wu Z, Johnston KE, Arnold FH, Yang KK. Wu Z, et al. Curr Opin Chem Biol. 2021 Dec;65:18-27. doi: 10.1016/j.cbpa.2021.04.004. Epub 2021 May 26. Curr Opin Chem Biol. 2021. PMID: 34051682 Free article. Review.
Machine Learning for Protein Engineering.
Johnston KE, Fannjiang C, Wittmann BJ, Hie BL, Yang KK, Wu Z. Johnston KE, et al. Among authors: wu z. ArXiv [Preprint]. 2023 May 26:arXiv:2305.16634v1. ArXiv. 2023. PMID: 37292483 Free PMC article. Preprint.
Highly accurate protein structure prediction for the human proteome.
Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, Figurnov M, Ronneberger O, Bates R, Kohl SAA, Potapenko A, Ballard AJ, Romera-Paredes B, Nikolov S, Jain R, Clancy E, Reiman D, Petersen S, Senior AW, Kavukcuoglu K, Birney E, Kohli P, Jumper J, Hassabis D. Tunyasuvunakool K, et al. Among authors: wu z. Nature. 2021 Aug;596(7873):590-596. doi: 10.1038/s41586-021-03828-1. Epub 2021 Jul 22. Nature. 2021. PMID: 34293799 Free PMC article.
Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. Abramson J, et al. Among authors: wu z. Nature. 2024 May 8. doi: 10.1038/s41586-024-07487-w. Online ahead of print. Nature. 2024. PMID: 38718835
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