King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887

Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948

Naseri-Nosar P, Nogalski M, Shenk T. The aryl hydrocarbon receptor facilitates the human cytomegalovirus-mediated G1/S block to cell cycle progression. Proc Natl Acad Sci U S A. 2021;118(12). PMCID: PMC8000196

Xie Q, Wiedmann M, Zhao A, Pagan I, Novick R, Suga H, Muir T. Discovery of quorum quenchers targeting the membrane-embedded sensor domain of the receptor histidine kinase, AgrC. Chem Commun (Camb). 2020;56(76):11223–11226. PMCID: PMC7530097

McCready A, Paczkowski J, Henke B, Bassler B. Structural determinants driving homoserine lactone ligand selection in the LasR quorum-sensing receptor. Proc Natl Acad Sci U S A. 2019;116(1):245–254. PMCID: PMC6320529

Zhao Y, Huang G, Wu J, Wu Q, Gao S, Yan Z, Lei J, Yan N. Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca Channel. Cell. 2019;177(6):1495–1506.e12. PMID: 31150622

Huang X, Duddy O, Silpe J, Paczkowski J, Cong J, Henke B, Bassler B. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020;295(10):2916–2931. PMCID: PMC7062168

Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845

Qian H, Cao P, Hu M, Gao S, Yan N, Gong X. Inhibition of tetrameric Patched1 by Sonic Hedgehog through an asymmetric paradigm. Nat Commun. 2019;10(1):2320. PMCID: PMC6534611

Paczkowski J, McCready A, Cong J-P, Li Z, Jeffrey P, Smith C, Henke B, Hughson F, Bassler B. An Autoinducer Analogue Reveals an Alternative Mode of Ligand Binding for the LasR Quorum-Sensing Receptor. ACS Chem Biol. 2019;14(3):378–389. PMCID: PMC6601336

Gong X, Qian H, Cao P, Zhao X, Zhou Q, Lei J, Yan N. Structural basis for the recognition of Sonic Hedgehog by human Patched1. Science. 2018;361(6402). PMID: 29954986

Chakrabarti R, Celià-Terrassa T, Kumar S, Hang X, Wei Y, Choudhury A, Hwang J, Peng J, Nixon B, Grady J, DeCoste C, Gao J, van Es J, Li M, Aifantis I, Clevers H, Kang Y. Notch ligand Dll1 mediates cross-talk between mammary stem cells and the macrophageal niche. Science. 2018;360(6396). PMCID: PMC7881440

Remillard D, Buckley D, Paulk J, Brien G, Sonnett M, Seo H-S, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong S, Bradner J. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 2017;56(21):5738–5743. PMCID: PMC5967236

Hao Q, Yin P, Yan C, Yuan X, Li W, Zhang Z, Liu L, Wang J, Yan N. Functional mechanism of the abscisic acid agonist pyrabactin. J Biol Chem. 2010;285(37):28946–52. PMCID: PMC2937921

Deng D, Xu C, Sun P, Wu J, Yan C, Hu M, Yan N. Crystal structure of the human glucose transporter GLUT1. Nature. 2014;510(7503):121–5. PMID: 24847886

Deng D, Sun P, Yan C, Ke M, Jiang X, Xiong L, Ren W, Hirata K, Yamamoto M, Fan S, Yan N. Molecular basis of ligand recognition and transport by glucose transporters. Nature. 2015;526(7573):391–6. PMID: 26176916

Deshpande G, Manry D, Jourjine N, Mogila V, Mozes H, Bialistoky T, Gerlitz O, Schedl P. Role of the ABC transporter Mdr49 in Hedgehog signaling and germ cell migration. Development. 2016;143(12):2111–20. PMCID: PMC4920174

Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics. 2014;30(14):2081–3. PMCID: PMC4080744

Seyedsayamdost M, Traxler M, Zheng S-L, Kolter R, Clardy J. Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc. 2011;133(30):11434–7. PMCID: PMC3144690

McBride C, Baier F, Omondi A, Spitzer S, Lutomiah J, Sang R, Ignell R, Vosshall L. Evolution of mosquito preference for humans linked to an odorant receptor. Nature. 2014;515(7526):222–7. PMCID: PMC4286346

Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci. 2007;16(11):2317–33. PMCID: PMC2211703

Miller S, Xavier K, Campagna S, Taga M, Semmelhack M, Bassler B, Hughson F. Salmonella typhimurium recognizes a chemically distinct form of the bacterial quorum-sensing signal AI-2. Mol Cell. 2004;15(5):677–87. PMID: 15350213

Neiditch M, Federle M, Pompeani A, Kelly R, Swem D, Jeffrey P, Bassler B, Hughson F. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell. 2006;126(6):1095–108. PMCID: PMC3468944

Ng W-L, Wei Y, Perez L, Cong J, Long T, Koch M, Semmelhack M, Wingreen N, Bassler B. Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules. Proc Natl Acad Sci U S A. 2010;107(12):5575–80. PMCID: PMC2851778

Chen G, Swem L, Swem D, Stauff D, O’Loughlin C, Jeffrey P, Bassler B, Hughson F. A strategy for antagonizing quorum sensing. Mol Cell. 2011;42(2):199–209. PMCID: PMC3092643

Wei Y, Ng W-L, Cong J, Bassler B. Ligand and antagonist driven regulation of the Vibrio cholerae quorum-sensing receptor CqsS. Mol Microbiol. 2012;83(6):1095–108. PMCID: PMC3310172