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Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.
Zhu D, Brookes DH, Busia A, Carneiro A, Fannjiang C, Popova G, Shin D, Donohue KC, Lin LF, Miller ZM, Williams ER, Chang EF, Nowakowski TJ, Listgarten J, Schaffer DV. Zhu D, et al. Among authors: brookes dh. Sci Adv. 2024 Jan 26;10(4):eadj3786. doi: 10.1126/sciadv.adj3786. Epub 2024 Jan 24. Sci Adv. 2024. PMID: 38266077 Free PMC article.
Improvements to the APBS biomolecular solvation software suite.
Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Jurrus E, et al. Among authors: brookes dh. Protein Sci. 2018 Jan;27(1):112-128. doi: 10.1002/pro.3280. Epub 2017 Oct 24. Protein Sci. 2018. PMID: 28836357 Free PMC article.
Finding Our Way in the Dark Proteome.
Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Bhowmick A, et al. Among authors: brookes dh. J Am Chem Soc. 2016 Aug 10;138(31):9730-42. doi: 10.1021/jacs.6b06543. Epub 2016 Jul 19. J Am Chem Soc. 2016. PMID: 27387657 Free PMC article.