Kuhlman, Brian

Comprehensive List

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Selected recent publications by topic 

Computational methods for protein design 

• Randolph NZ, Kuhlman B. Invariant point message passing for protein side chain packing. Proteins. 2024 Oct;92(10):1220-1233. doi: 10.1002/prot.26705. Epub 2024 May 24. PMID: 38790143; PMCID: PMC11511640. 
• Dieckhaus H, Brocidiacono M, Randolph NZ, Kuhlman B. Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proc Natl Acad Sci U S A. 2024 Feb 6;121(6):e2314853121. doi: 10.1073/pnas.2314853121. Epub 2024 Jan 29. PMID: 38285937; PMCID: PMC10861915. 

Protein switch design 

• Kudo S, Kuhlman B. De novo masking domains that gate TNF-family ligand assembly and activity. bioRxiv [Preprint]. 2026 Apr 22:2026.04.20.719557. doi: 10.64898/2026.04.20.719557. PMID: 42079277; PMCID: PMC13131590. 
• McCue AC, Demarest SJ, Froning KJ, Hickey MJ, Antonysamy S, Kuhlman B. Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy. MAbs. 2024 Jan-Dec;16(1):2373325. doi: 10.1080/19420862.2024.2373325. Epub 2024 Jul 4. PMID: 38962811; PMCID: PMC11225918. 
• Goudy OJ, Nallathambi A, Kinjo T, Randolph NZ, Kuhlman B. In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models. Proc Natl Acad Sci U S A. 2023 Dec 5;120(49):e2307371120. doi: 10.1073/pnas.2307371120. Epub 2023 Nov 30. PMID: 38032933; PMCID: PMC10710080. 

Vaccine design

• Phan TTN, Thiono DJ, Hvasta MG, Shah RP, Ajo GP, Huang WC, Lovell JF, Tian S, de Silva AM, Kuhlman B. Multivalent administration of dengue E dimers on liposomes elicits type-specific neutralizing responses without immune interference. NPJ Vaccines. 2025 Jun 9;10(1):119. doi: 10.1038/s41541-025-01179-w. PMID: 40490495; PMCID: PMC12149311. 
• Phan TTN, Hvasta MG, Kudlacek ST, Thiono DJ, Tripathy A, Nicely NI, de Silva AM, Kuhlman B. A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines. J Biol Chem. 2022 Jul;298(7):102079. doi: 10.1016/j.jbc.2022.102079. Epub 2022 May 26. PMID: 35643320; PMCID: PMC9249817. 
• Kudlacek ST, Metz S, Thiono D, Payne AM, Phan TTN, Tian S, Forsberg LJ, Maguire J, Seim I, Zhang S, Tripathy A, Harrison J, Nicely NI, Soman S, McCracken MK, Gromowski GD, Jarman RG, Premkumar L, de Silva AM, Kuhlman B. Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Sci Adv. 2021 Oct 15;7(42):eabg4084. doi: 10.1126/sciadv.abg4084. Epub 2021 Oct 15. PMID: 34652943; PMCID: PMC8519570. 

Enzyme design 

• Shelby C, Kuzelka KP, Ellis JM, Yao Z, McCue AC, Park R, Nair SK, Bowers A, Kuhlman B. Enhancing Enzymatic Bioconjugation Efficiency via Computer-Based Installation of a Substrate Recruitment Domain. Bioconjug Chem. 2026 Apr 15;37(4):699-712. doi: 10.1021/acs.bioconjchem.5c00468. Epub 2026 Mar 17. PMID: 41844172; PMCID: PMC13186416. 
• Park R, Ongpipattanakul C, Nair SK, Bowers AA, Kuhlman B. Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nat Chem Biol. 2023 Apr;19(4):460-467. doi: 10.1038/s41589-022-01206-0. Epub 2022 Dec 12. PMID: 36509904; PMCID: PMC10065947.