Recent Publications

Bao F, Li L, et al Altschuler SJ, Wu LF. Transitive prediction of small-molecule function through alignment of high-content screening resources. Nat Biotechnol (2025). 

 

Li L, et al & Altschuler SJ, Wu LF. A phenopushing platform to identify compounds that alleviate acute hypoxic stress by fast-tracking cellular adaptation. Nat Commun 16, 2684 (2025).

 

Sun, X., Wu, L.F., Altschuler, S.J. & Hata AN. Targeting therapy-persistent residual disease. Nat Cancer 5, 1298–1304 (2024). 

 

Konstantinidou M, Virta JM, Arkin MR. Stabilization of Native Protein-Protein Interactions with Molecular Glues: A 14-3-3 Case Study. Acc Chem Res. 2025 Sep 16;58(18):2840-2851. PMID: 40910885; PMCID: PMC12444995.

 

Konstantinidou M, et al. & Arkin MR. Scaffold-hopping for molecular glues targeting the 14-3-3/ERα complex. Nat Commun. 2025 Jul 14;16(1):6467. PMID: 40659654; PMCID: PMC12260087. 

 

Li F, Eriksen J, et al. Burlingame A, Grabe M, Stroud RM, Edwards RH.  Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2. Nat Struct Mol Biol. 2025 Aug;32(8):1479-1487.  PMID: 40461871 

 

Zahavi EE, et al., Burlingame AL, Fainzilber M. Repeat-element RNAs integrate a neuronal growth circuit. Cell. 2025 Aug 7;188(16):4350-4365.e22. PMID: 40381624.  

 

Detomasi TC, et al., Renslo AR, Craik CS. Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy. Sci Adv. 2025 Apr 25;11(17):eadt7836.. PMID: 40267184; PMCID: PMC12017303. 

 

Hou K, Huang W, Qi M, Tugwell TH, Alturaifi TM, Chen Y, Zhang X, Lu L, Mann SI, Liu P, Yang Y, DeGrado WF. De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts. Science. 2025 May 8;388(6747):665-670. PMID: 40339022; PMCID: PMC12316402. 

 

Grau B, Kormos R, et al., DeGrado WF, Mingarro I. Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes. Sci Adv. 2025 Feb 21;11(8):eads6804. PMID: 39970206; PMCID: PMC11837994.

 

Lu L,  et al & DeGrado WF. De novo design of drug-binding proteins with predictable binding energy and specificity. Science. 2024 Apr 5;384(6691):106-112. PMID: 38574125; PMCID: PMC11290694. 

 

Mravic M, et al., DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol. 2024 Jun;20(6):751-760. PMID: 38480980; PMCID: PMC11142920. 

 

Bibel B, et al., Fraser JS, Fujimori DG. Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. Nucleic Acids Res. 2025 Jan 24;53(3) PMID: 39907106; PMCID: PMC11795202.  

 

Huycke TR, et al & Gartner ZJ. Patterning and folding of intestinal villi by active mesenchymal dewetting. Cell. 2024 Jun 6;187(12):3072-3089.e20. PMID: 38781967; PMCID: PMC11166531. 

 

Carroll EC, et al & Gestwicki JE. High-throughput discovery of fluoroprobes that recognize amyloid fibril polymorphs. Nat Chem. 2025 Oct;17(10):1565-1575. PMID: 40813616; PMCID: PMC12491066. 

 

Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Nat Struct Mol Biol. 2024 Dec;31(12):1848-1858. PMID: 38951622; PMCID: PMC11638070. 

 

Wu T, et al. & Gestwicki JE. Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes. Nat Biotechnol. 2025 Jan;43(1):106-113. PMID: 38744946; PMCID: PMC12285679.

 

Moss FR et al & Grabe M, Frost A. Brominated lipid probes expose structural asymmetries in constricted membranes. Nat Struct Mol Biol. 2023 Feb;30(2):167-175. PMID: 36624348; PMCID: PMC9935397. 

 

Meyer K, et al. & Huang B, Weiner OD. YAP charge patterning mediates signal integration through transcriptional co-condensates. Nat Commun. 2025 Aug 12;16(1):7454. PMID: 40796733; PMCID: PMC12343768. 

 

Howard MK, et al. & Coyote-Maestas W, Manglik A. Molecular basis of proton sensing by G protein-coupled receptors. Cell. 2025 Feb 6;188(3):671-687.e20. PMID: 39753132; PMCID: PMC11849372. 

 

de March CA, et al & Manglik A, Matsunami H. Engineered odorant receptors illuminate the basis of odour discrimination. Nature. 2024 Nov;635(8038):499-508. PMID: 39478229. 

 

Hoppe N, et al &  Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol. 2024 Apr;31(4):667-677. PMID: 38326651; PMCID: PMC11221913.

 

Klope MT, et al & Renslo AR. Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance. Sci Adv. 2025 Aug 8;11(32):eads9168. PMID: 40779626; PMCID: PMC12333675.  

 

Correy GJ, Rachman MM, et al. & Renslo AR, Walters WP, Fraser JS. Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning. Sci Adv. 2025 May 30;11(22):eads7187. PMID: 40435250; PMCID: PMC12118597. 

 

Tummino TA, et al., Basbaum AI, Shoichet BK. Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects. Nat Commun. 2025 Mar 6;16(1):2237. PMID: 40044644; PMCID: PMC11882969.

 

Liu F, Mailhot O, et al., Irwin JJ, Shoichet BK. The impact of library size and scale of testing on virtual screening. Nat Chem Biol. 2025 Jul;21(7):1039-1045. PMID: 39753705; PMCID: PMC12229919. 

 

Liu F, et al & Shoichet BK, Skiniotis G. Large library docking identifies positive allosteric modulators of the calcium-sensing receptor. Science. 2024 Sep 20;385:eado1868. PMID: 39298584; PMCID: PMC11629082. 

 

Lyu J, et al & Skiniotis G, Kruse AC, Shoichet BK, Roth BL. AlphaFold2 structures guide prospective ligand discovery. Science. 2024 Jun 21;384(6702):eadn6354. PMID: 38753765; PMCID: PMC11253030. 

 

Yang J, et al & Shu X. MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol. 2024 Oct;31(10):1567-1579. PMID: 38811792; PMCID: PMC11479839. 

 

Sun W, et al & Wang L. Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem. 2023 Jan;15(1):21-32. PMID: 36202986; PMCID: PMC9840682. 

 

Lin Z, et al, & Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science. 2024 Jul 19;385(6706):eadl5763. PMID: 39024454; PMCID: PMC12517702. 

 

Zhou X, et al & Verba KA, Wells JA. Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4. Nat Chem Biol. 2024 Jun;20(6):742-750. PMID: 38308046; PMCID: PMC11142921.

 

Solomon PE, et al & Wells JA. Discovery of VH domains that allosterically inhibit ENPP1. Nat Chem Biol. 2024 Jan;20(1):30-41 PMCID: PMC10746542. 

 

Michael J Boucher et al & Zaro BW, Hiten D Madhan. Phenotypic landscape of an invasive fungal pathogen reveals its unique biology.  Cell188, 4003-4025 (2025).