Functional Protein Design Lab

23. L. Tran, S. Sharma, S. Klein, D. Jurgens, J. Decarreau, B. Liu, Y. Wang, A. Bera, A. Kang, J. Woods, E. Joyce, D. Vafeados, N. Roullier, W. Chen, G. Lee, J. Mahamid, L. Lavis, L. An*, D. Baker*. Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging, 2025, biorXiv, doi: https://doi.org/10.1101/2025.08.03.668343.

Design of orthogonal fluorophore-binding proteins for multiplex imaging applications.

Preprint

22. I. Anishchenko, Y. Kipnis, I. Kalvet, G. Zhou, R. Krishna, S.J. Pellock, A. Lauko, G.R. Lee, L. An, J. Dauparas, F. DiMaio, & D. Baker, Modeling protein–small molecule conformational ensembles with PLACER, 2025, Proc. Natl. Acad. Sci. U.S.A. 122 (45) e2427161122.

Development of PLACER for modeling protein-small molecule conformational ensembles.

on PNAS

21. G. Li#*, L. An#, W. Yang#, L. Yang, T. Wei, J. Shi, J. Wang, J. Doonan, K. Xie, A. R. Fernie, E. S. Lagudah, R. A. Wing, C. Gao*. Integrated biotechnological and AI innovations for crop improvement, 2025, Nature, 643, 925.

Comprehensive review of integrated biotechnological and AI approaches for crop improvement.

on Nature

20. J. Dauparas, G. Lee, R. Pecoraro, L. An, I. Anishchenko, C. Glasscock, D. Baker*, Atomic context-conditioned protein sequence design using LigandMPNN, 2025, Nature Methods, Accepted, https://doi.org/10.1038/s41592-025-02626-1.

Development of a neural network for ligand-aware protein sequence design.

on Nature Methods

19. L. An*, M. Seid, L. Tran, S. Majumder, I. Goreshnik, G. Lee, J. Dauparas, I. Anishchenko, B. Coventry, A. Bera, A. Kang, P. M. Levine, V. Alvarez, A. Pillai, C. Norn, D. Feldman, D. Zorine, D. R. Hicks, X. Li, M. G. Sanchez, D. K. Vafeados, P. J. Salveson, A. A. Vorobieva, and D. Baker*. Binding and sensing diverse small molecules using shape complementary pseudocycles, 2024, Science, 385, 276.

Design of protein-based sensors for small molecule detection using shape complementary pseudocycles.

18. L. An#*, D. Hicks#, D. Zorine#, J. Dauparas, B. Wicky, L. Milles, A. Courbet, A. Bera, H. Nguyen, A. Kang, L. Carter, D. Baker*. Hallucination of closed repeat proteins containing central pockets, Nat. Struct. Mol. Biol., 2023, 30, 1755.

Computational design of novel proteins with central binding pockets using deep learning approaches.

on Nature Structural & Molecular Biology

17. L. An#, D. Cogan#, C. Navo, G. Jiménez-Osés, S. K. Nair, and W. A. van der Donk*, Substrate-assisted enzymatic formation of lysinoalanine in duramycin, Nat. Chem. Biol. 2018, 10, 928.

Elucidation of the mechanism of lysinoalanine formation in duramycin biosynthesis.

on Nature Chemical Biology

16. L. An#* and G. R. Lee#*, De novo protein design using the blueprint builder in Rosetta, Current Protocols in Protein Science, 2020, 102,1, e116.

Protocol for de novo protein design using the Rosetta blueprint builder.

on Current Protocols

15. L. An, and W. A. van der Donk*, Recent progress in lanthipeptide biosynthesis, discovery, and engineering, Comprehensive Natural Products III. 2019, 2, 119.

Comprehensive review of lanthipeptide biosynthesis, discovery, and engineering approaches.

on Comprehensive Natural Products III

14. L. An, M. Rehan H. Shah Gilani, G. L. Liang*, Peptide-based nanostructures for cancer diagnosis and therapy, Curr. Med. Chem. 2014, 21, 2453.

Review of peptide-based nanostructures for cancer diagnosis and therapy applications.

on Current Medicinal Chemistry

13. J. Acedo, I. Bothwell, L. An, A. Trouth, C. Frazier, W. A. van der Donk*, O-Methyltransferase-mediated Incorporation of a β-Amino Acid in Lanthipeptides, J. Am. Chem. Soc. 2019, 141, 42, 16790.

Mechanistic study of β-amino acid incorporation in lanthipeptides by O-methyltransferase.

on JACS

12. L. An, "iGEM: Get & Give (& Share)", Microbiology Today, Web. 15 May 2018.

Perspective on knowledge sharing and collaboration in the iGEM competition.

on Microbiology Today

11. Y. Liu#, Q. Miao#, P. Zou, L. Liu, X. Wang, L. An, X. Zhang, X. Qian, S. Luo, and G. Liang*. Enzyme-controlled intracellular self-assembly of 18F nanoparticles for enhanced microPET imaging of tumor. Theranostics. 2015, 5, 1058.

Development of enzyme-responsive 18F nanoparticles for improved tumor imaging.

on Theranostics

10. Y. Yuan#, L. Wang#, W. Du, Z. Ding, J. Zhang, T. Han, L. An, H. Zhang, and G. Liang*. Intracellular self-assembly of taxol nanoparticles for overcoming multi-drug resistance. Angew. Chem. Int. Ed. 2015, 54, 9700.

Development of intracellular self-assembling taxol nanoparticles to overcome drug resistance.

on Angewandte Chemie

9. Y. Yuan, J. Zhang, Q. Cao, L. An, G. Liang*. Intracellular disassembly of self-quenched nanoparticles turns NIR fluorescence on for sensing furin activity in cells and in tumors. Anal. Chem. 2015, 87, 6180.

Development of self-quenched nanoparticles for NIR fluorescence-based furin activity sensing.

on Analytical Chemistry

8. Y. Yuan, S. Ge, H. Sun, X. Dong, H. Zhao, L. An, J. Zhang, J. Wang, B. Hu, G. Liang*. Intracellular self-assembly and disassembly of 19F nanoparticles confer respective "Off" and "On" 19F NMR/MRI signals for legumain activity detection in zebrafish. ACS Nano. 2015, 9, 5117-5124.

Development of 19F NMR/MRI probes for legumain activity detection in zebrafish.

on ACS Nano

7. Y. Yuan#, H. Sun#, S. Ge#, M. Wang, H. Zhao, L. Wang, L. An, J. Zhang, H. Zhang, B. Hu, J. Wang, G. Liang*. Controlled intracellular self-assembly and disassembly of 19F nanoparticles for MR imaging of caspase 3/7 in zebrafish. ACS Nano. 2015, 9, 761.

Development of 19F nanoparticles for caspase 3/7 activity imaging in zebrafish.

on ACS Nano

6. W. Wang#, J. Qian#, A. Tang#, L. An, K. Zhong, G. Liang*. Using magnetic resonance imaging to study enzymatic hydrogelation. Anal. Chem. 2014, 86, 5955-5961.

Application of magnetic resonance imaging for studying enzymatic hydrogelation processes.

on Analytical Chemistry

5. Y. Yuan, J. Zhang, L. An, Q. Cao, Y Deng, G. Liang*. Oligomeric nanoparticles functionalized with NIR-emitting CdTe/CdS QDs and folate for tumor-targeted imaging. Biomaterials. 2014, 35, 7881.

Development of folate-targeted oligomeric nanoparticles with NIR-emitting quantum dots for tumor imaging.

on Biomaterials

4. Y. Yuan, S. Jiang, Q. Miao, J. Zhang, M. Wang, L. An, Q. Cao, Y. Guan, Q. Zhang, G. Liang*, Fluorescent switch for fast and selective detection of mercury (II) ions in vitro and in living cells and a simple device for its removal. Talanta. 2014, 125, 204.

Development of a fluorescent switch for mercury detection and removal in biological systems.

on Talanta

3. B. You*, P. Yin, and L. An. Multifunctional Electroactive Heteroatom-Doped Carbon Aerogels. Small, 2014, 10: 4352-4361.

Development of multifunctional electroactive carbon aerogels with heteroatom doping.

on Small

2. Y. Deng, Y. Luo, L. An, Y. Yue, M. Rehan H. Shah Gilani, G. Liang*. Covalently conjugating fluorescence probes to nanoparticles for signal enhancement, Chem. Lett. 2013, 42, 10, 130424.

Development of covalent conjugation methods for fluorescence probe attachment to nanoparticles.

on Chemistry Letters

1. Y. Yuan., X. Wang, B. Mei, D. Zhang, L. An, X. He, J. Jiang, G. Liang*, Labeling thiols on proteins, living cells, and tissues with enhanced emission induced by FRET, Sci. Rep. 2013, 3, 3523.

Development of FRET-based labeling methods for thiol detection in biological systems.

on Scientific Reports

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