Lu Lab Tsinghua Protein Design Center

Publications

For a complete and up-to-date list of publications from the Lu Lab, please visit Google Scholar.

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2026

Figure 1 from Emergence of specific binding and catalysis from a designed generalist binding protein Figure 1
Emergence of specific binding and catalysis from a designed generalist binding protein
Yuda Chen, Sagar Bhattacharya, Lena Bergmann, Galen J. Correy, Sophia K. Tan, …, Alexander N. Volkov, Ivan V. Korendovych, Nicholas F. Polizzi, James S. Fraser, William F. DeGrado
Nature Chemistry  ·  04 May 2026  ·  doi:10.1038/s41557-026-02125-6

2025

Figure 1 from De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy Figure 1
De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy
Yuda Chen, Klaus Yserentant, Kibeom Hong, Yiming Kuang, Arghya Bhowmick, …, Jonathan B. Grimm, Luke D. Lavis, R. Dyche Mullins, William F. DeGrado, Bo Huang
openRxiv  ·  25 Jun 2025  ·  doi:10.1101/2025.06.24.661379
Figure 1 from De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts Figure 1
De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts
Kaipeng Hou, Wei Huang, Miao Qi, Thomas H. Tugwell, Turki M. Alturaifi, …, Lei Lu, Samuel I. Mann, Peng Liu, Yang Yang, William F. DeGrado
Science  ·  08 May 2025  ·  doi:10.1126/science.adt7268

2024

Figure 1 from SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex Figure 1
SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex
Lee Schnaider, Sophia Tan, Pratik R. Singh, Floriana Capuano, Alistair J. Scott, …, Lei Lu, Hyunjun Yang, E. Jayne Wallace, Hyunil Jo, William F. DeGrado
Journal of the American Chemical Society  ·  27 Aug 2024  ·  doi:10.1021/jacs.4c07920
Figure 1 from De novo design of drug-binding proteins with predictable binding energy and specificity Figure 1
De novo design of drug-binding proteins with predictable binding energy and specificity
Lei Lu, Xuxu Gou, Sophia K. Tan, Samuel I. Mann, Hyunjun Yang, …, Yibing Wu, Morgan E. Diolaiti, Alan Ashworth, Nicholas F. Polizzi, William F. DeGrado
Science  ·  05 Apr 2024  ·  doi:10.1126/science.adl5364
Drug-binding protein design.

2021

Figure 1 from Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics Figure 1
Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics
Lei Lu, Mark Scalf, Michael R. Shortreed, Lloyd M. Smith
Journal of the American Society for Mass Spectrometry  ·  23 Mar 2021  ·  doi:10.1021/jasms.0c00462
Figure 1 from Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus Figure 1
Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus
Michael R. Shortreed, Robert J. Millikin, Lei Liu, Zach Rolfs, Rachel M. Miller, Leah V. Schaffer, Brian L. Frey, Lloyd M. Smith
Journal of Proteome Research  ·  08 Mar 2021  ·  doi:10.1021/acs.jproteome.0c00838

2020

Figure 1 from O-Pair Search with MetaMorpheus for O-glycopeptide characterization Figure 1
O-Pair Search with MetaMorpheus for O-glycopeptide characterization
Lei Lu, Nicholas M. Riley, Michael R. Shortreed, Carolyn R. Bertozzi, Lloyd M. Smith
Nature Methods  ·  26 Oct 2020  ·  doi:10.1038/s41592-020-00985-5
Figure 1 from Spritz: A Proteogenomic Database Engine Figure 1
Spritz: A Proteogenomic Database Engine
Anthony J. Cesnik, Rachel M. Miller, Khairina Ibrahim, Lei Lu, Robert J. Millikin, Michael R. Shortreed, Brian L. Frey, Lloyd M. Smith
Journal of Proteome Research  ·  23 Sep 2020  ·  doi:10.1021/acs.jproteome.0c00407
Figure 1 from O-Pair Search with MetaMorpheus for O-glycopeptide Characterization Figure 1
O-Pair Search with MetaMorpheus for O-glycopeptide Characterization
Lei Lu, Nicholas M. Riley, Michael R. Shortreed, Carolyn R. Bertozzi, Lloyd M. Smith
openRxiv  ·  20 May 2020  ·  doi:10.1101/2020.05.18.102327

2019

Figure 1 from HOTMAQ: A Multiplexed Absolute Quantification Method for Targeted Proteomics Figure 1
HOTMAQ: A Multiplexed Absolute Quantification Method for Targeted Proteomics
Xiaofang Zhong, Qinying Yu, Fengfei Ma, Dustin C. Frost, Lei Lu, Zhengwei Chen, Henrik Zetterberg, Cynthia Carlsson, Ozioma Okonkwo, Lingjun Li
Analytical Chemistry  ·  04 Jan 2019  ·  doi:10.1021/acs.analchem.8b04580

2018

Figure 1 from Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus Figure 1
Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus
Lei Lu, Robert J. Millikin, Stefan K. Solntsev, Zach Rolfs, Mark Scalf, Michael R. Shortreed, Lloyd M. Smith
Journal of Proteome Research  ·  25 May 2018  ·  doi:10.1021/acs.jproteome.8b00141