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Ye, M., Chen, E. V., Pfeil, S. H., Martin, K. N., Atrafi, T., Yun, S., Martinez, Z., and Yatsunyk, L. A. (2022) Homopurine guanine-rich sequences in complex with N-methyl mesoporphyrin IX form parallel G-quadruplex dimers and display a unique symmetry tetrad. Bioorg Med Chem. 77, 117112
Ye, Q., Kim, D. Hyun, Dereli, I., Rosenberg, S. C., Hagemann, G., Herzog, F., Tóth, A., Cleveland, D. W., and Corbett, K. D. (2017) The AAA+ ATPase TRIP13 remodels HORMA domains through N-terminal engagement and unfolding. EMBO J. 10.15252/embj.201797291
Ye, J., and Van den Berg, B. (2004) Crystal structure of the bacterial nucleoside transporter Tsx. EMBO J. 23, 3187-95
Ye, Q., Lu, S., and Corbett, K. D. (2021) Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol. 12, 719037
Ye, Q., Lau, R. K., Mathews, I. T., Birkholz, E. A., Watrous, J. D., Azimi, C. S., Pogliano, J., Jain, M., and Corbett, K. D. (2019) HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. Mol Cell. 10.1016/j.molcel.2019.12.009
Ye, Q., West, A. M. V., Silletti, S., and Corbett, K. D. (2020) Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Protein Sci. 10.1002/pro.3909
Ye, W., Paul, D., Gao, L., Seckute, J., Sangaiah, R., Jayaraj, K., Zhang, Z., P Kaminski, A., Ealick, S. E., Gold, A., and Ball, L. M. (2014) Ethenoguanines undergo glycosylation by nucleoside 2'-deoxyribosyltransferases at non-natural sites. PLoS One. 9, e115082
Ye, Q., Ur, S. N., Su, T. Y., and Corbett, K. D. (2016) Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator. EMBO J. 35, 2139-2151
Ye, Q., West, A. M. V., Silletti, S., and Corbett, K. D. (2020) Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. bioRxiv. 10.1101/2020.05.17.100685
Ye, G., Gallant, J., Zheng, J., Massey, C., Shi, K., Tai, W., Odle, A., Vickers, M., Shang, J., Wan, Y., Du, L., Aihara, H., Perlman, S., LeBeau, A., and Li, F. (2021) The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates. Elife. 10.7554/eLife.64815
Yee, E. F., Dzikovski, B., and Crane, B. R. (2019) Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping. J Am Chem Soc. 141, 17571-17587
Yelshanskaya, M. V., Singh, A. K., Narangoda, C., Williams, R. S. B., Kurnikova, M. G., and Sobolevsky, A. I. (2020) Structural basis of AMPA receptor inhibition by 4-BCCA. Br J Pharmacol. 10.1111/bph.15254
Yelshanskaya, M. V., Li, M., and Sobolevsky, A. I. (2014) Structure of an agonist-bound ionotropic glutamate receptor. Science. 345, 1070-4
Yelshanskaya, M. V., Singh, A. K., Sampson, J. M., Narangoda, C., Kurnikova, M., and Sobolevsky, A. I. (2016) Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs. Neuron. 91, 1305-15
Yi, C., Chen, B., Qi, B., Zhang, W., Jia, G., Zhang, L., Li, C. J., Dinner, A. R., Yang, C. - G., and He, C. (2012) Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol. 19, 671-6
Yildiz, M., Ghosh, S., Bell, J. A., Sherman, W., and Hardy, J. A. (2013) Allosteric inhibition of the NS2B-NS3 protease from dengue virus. ACS Chem Biol. 8, 2744-52
Yin, L., Shi, K., and Aihara, H. (2023) Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat Struct Mol Biol. 10.1038/s41594-023-01034-3
Yin, Y., Romei, M. G., Sankar, K., Pal, L. R., Hoi, K. Hon, Yang, Y., Leonard, B., Boenig, G. De Leon, Kumar, N., Matsumoto, M., Payandeh, J., Harris, S. F., Moult, J., and Lazar, G. A. (2022) Antibody interfaces revealed through structural mining. Comput Struct Biotechnol J. 20, 4952-4968
Yin, Z., Shi, K., Banerjee, S., Pandey, K. K., Bera, S., Grandgenett, D. P., and Aihara, H. (2016) Crystal structure of the Rous sarcoma virus intasome. Nature. 530, 362-6
Yin, F. Fang, Bailey, S., C Innis, A., Ciubotaru, M., Kamtekar, S., Steitz, T. A., and Schatz, D. G. (2009) Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat Struct Mol Biol. 16, 499-508
Yin, Q., Sester, D. P., Tian, Y., Hsiao, Y. - S., Lu, A., Cridland, J. A., Sagulenko, V., Thygesen, S. J., Choubey, D., Hornung, V., Walz, T., Stacey, K. J., and Wu, H. (2013) Molecular mechanism for p202-mediated specific inhibition of AIM2 inflammasome activation. Cell Rep. 4, 327-39
Yirmiya, E., Leavitt, A., Lu, A., Ragucci, A. E., Avraham, C., Osterman, I., Garb, J., Antine, S. P., Mooney, S. E., Hobbs, S. J., Kranzusch, P. J., Amitai, G., and Sorek, R. (2024) Phages overcome bacterial immunity via diverse anti-defence proteins. Nature. 625, 352-359
Yirmiya, E., Hobbs, S. J., Leavitt, A., Osterman, I., Avraham, C., Hochhauser, D., Madhala, B., Skovorodka, M., Tan, J. M. J., Toyoda, H. C., Chebotar, I., Itkin, M., Malitsky, S., Amitai, G., Kranzusch, P. J., and Sorek, R. (2025) Structure-guided discovery of viral proteins that inhibit host immunity. Cell. 10.1016/j.cell.2024.12.035
Yockey, O. P., Jha, V., Ghodke, P. P., Xu, T., Xu, W., Ling, H., Pradeepkumar, P. I., and Zhao, L. (2017) Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.. Chem Res Toxicol. 10.1021/acs.chemrestox.7b00227
Yoder, N., Yoshioka, C., and Gouaux, E. (2018) Gating mechanisms of acid-sensing ion channels. Nature. 10.1038/nature25782

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