Publications from the Lyu Lab

Preprint · 2026

Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery

Zhang J†, Yang C†, Zhang Y†, Chen X†, Lam B†, Bryant C†, Pidathala S, Wang Y, Moroz YS, Radchenko DS, Alon A*, Lee C-H*, Zhang Z*, Lyu J*

bioRxiv

Preprint · 2025

AlphaFold3 for Structure-guided Ligand Discovery

Menon KM†, Davasam A†, Chen G†, Bryant C†, Deng Z†, Lam B, Yang C, Barcelos D, Liu F, Alon A*, Lyu J*

bioRxiv

Science · 2024

AlphaFold2 structures guide prospective ligand discovery

Lyu J†*, Kapolka N†, Gumpper R†, Alon A†, Wang L†, Jain M, Alvarez X, Sakamoto K, Kim Y, DiBerto J, Kim K, Glenn IS, Tummino T, Huang S, Irwin J, Tarkhanova O, Moroz Y, Skiniotis G*, Kruse A*, Shoichet B*, Roth B*

Journal Commentary from In the Pipeline News in Nature

Preprint · 2026

A post-translational regulatory map of chronic antigen-driven human T cell dysfunction

Kojima H†, Wayne CR†, Somarribas Patterson LF†, Sanford H†, Chen T-J, Lin Y-H, Schoenfeld JD, McGary LHF, Chen Y-T, Kropp KN, … Menon KM, Hakimi AA, Lyu J, Klebanoff CA, Abdel-Wahab O, Vardhana SA*, Vinogradova EV*

bioRxiv

Cell Chemical Biology · 2025

Covalent targeting of splicing in T cells

Scott KA†, Kojima H†, Ropek N†, Warren CD†, Zhang TL, Hogg SJ, Sanford H, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O*, Vinogradova EV*

Science · 2024

Large library docking identifies positive allosteric modulators of the calcium-sensing receptor

Liu F†, Wu C-G†, Tu C-L, Glenn I, Meyerowitz J, Levit Kaplan A, Lyu J, Cheng Z, Tarkhanova OO, Moroz YS, Irwin JJ, Chang W*, Shoichet BK*, Skiniotis G*

Protein Science · 2023

Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors

Fink EA†, Bardine C†, Gahbauer S†, Singh I†, White K, Gu S, Wan X, Ary B, Glenn I, O’Connell J, O’Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, O’Donoghue AJ, Moroz Y, Taunton J, Renslo AR, Irwin JJ, García-Sastre A, Shoichet BK*, Craik CS*

Nature Chemical Biology · 2023

Modeling the expansion of virtual screening libraries

Lyu J, Irwin JJ*, Shoichet BK*

Journal Commentary from Artem Cherkasov Commentary from In the Pipeline

Nature Protocols · 2021

A practical guide to large-scale docking

Bender BJ†, Gahbauer S†, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK*

Nature · 2021

Structures of the σ2 receptor enable docking for bioactive ligand discovery

Alon A†, Lyu J†, Braz JM†, Tummino TA, Craik V, O’Meara MJ, Webb CM, Moroz YS, Huang X-P, Roth BL, Irwin JJ, Basbaum AI*, Shoichet BK*, Kruse AC*

Journal

Science · 2021

Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2

Tummino TA†, Rezelj VV†, Fischer B†, Fischer A†, O’Meara MJ, Monel B, Vallet T, Zhang Z, Alon A, O’Donnell HR, Lyu J, Schadt H, White KM, Krogan NJ, Urban L, Shokat K, Kruse A, García-Sastre A, Schwartz O, Moretti F*, Vignuzzi M*, Pognan F*, Shoichet BK*

Journal of Chemical Information and Modeling · 2021

Property-Unmatched Decoys in Docking Benchmarks

Stein RM, Yang Y, Balius TE, O’Meara MJ, Lyu J, Young J, Tang K, Shoichet BK*, Irwin JJ*

Cell · 2020

Structural insights into hallucinogen activation of Gq-coupled 5-HT2A serotonin receptors

Kim K, Che T, Panova O, DiBerto JF, Lyu J, Krumm BE, Wacker D, Robertson MJ, Seven AB, Nichols DE, Shoichet BK, Skiniotis G*, Roth BL*

Nature · 2020

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O’Meara MJ, … Lyu J, … Vignuzzi M*, García-Sastre A*, Shokat KM*, Shoichet BK*, Krogan NJ*

Nature · 2019

Ultra-large library docking for discovering new chemotypes

Lyu J†, Wang S†, Balius TE†, Singh I†, Levit A, Moroz YS, O’Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK*, Roth BL*, Irwin JJ*

Journal Commentary in Science Nature News and Views In the Pipeline Practical Fragments Blog Drug Target Review BiopharmaTrend NIH Press Release Nature Editorials Faculty of 1000

Journal of Medicinal Chemistry · 2018

Selectivity Challenges in Docking Screens for GPCR Targets and Anti-Targets

Weiss DR†, Karpiak J†, Huang X-P†, Sassano MF, Lyu J, Roth BL*, Shoichet BK*

Journal of Medicinal Chemistry · 2018

Design, Synthesis, and Biological Evaluation of Pyrimido[4,5-d]pyrimidine-2,4(1H,3H)-diones as Potent and Selective EGFR Inhibitors against L858R/T790M Resistance Mutation

Hao Y†, Lyu J†, Qu R†, Tong Y, Sun D, Feng F, Tong L, Yang T, Zhao Z, Zhu L, Ding J, Xu Y*, Xie H*, Li H*

Scientific Reports · 2017

Structure-Guided Design of C4-alkyl-1,4-dihydro-2H-pyrimido[4,5-d][1,3]oxazin-2-ones as Potent and Mutant-Selective EGFR L858R/T790M Inhibitors

Hao Y†, Lyu J†, Qu R†, Sun D, Zhao Z, Chen Z, Ding J, Xie H*, Xu Y*, Li H*

Oncotarget · 2016

Discovery of peptide inhibitors targeting human programmed death 1 (PD-1) receptor

Li Q†, Quan L†, Lyu J, He Z, Wang X, Meng J, Zhao Z, Zhu L*, Liu X*, Li H*

Journal of Medicinal Chemistry · 2016

Discovery and rational design of pteridin-7(8H)-one-based inhibitors targeting FMS-like tyrosine kinase 3 (FLT3) and its mutants

Sun D†, Yang Y†, Lyu J†, Zhou W, Zhao Z, Chen Z*, Xu Y*, Li H*

Bioorganic & Medicinal Chemistry · 2015

Antiproliferative and apoptosis-inducing activities of novel naphthalimide-cyclam conjugates through dual topoisomerase (topo) I/II inhibition

Tan S†, Sun D†, Lyu J†, Sun X, Wu F, Li Q, Yang Y, Liu J, Wang X, Chen Z, Li H*, Qian X*, Xu Y*

Publications

Selected publications

Complete list of publications