Publications

Found 1265 results
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Journal Article
Kümmel, D., Krishnakumar, S. S., Radoff, D. T., Li, F., Giraudo, C. G., Pincet, F., Rothman, J. E., and Reinisch, K. M. (2011) Complexin cross-links prefusion SNAREs into a zigzag array. Nat Struct Mol Biol. 18, 927-33
Kümmel, D., Krishnakumar, S. S., Radoff, D. T., Li, F., Giraudo, C. G., Pincet, F., Rothman, J. E., and Reinisch, K. M. (2011) Complexin cross-links prefusion SNAREs into a zigzag array. Nat Struct Mol Biol. 18, 927-33
Bryan, C. M., Rocklin, G. J., Bick, M. J., Ford, A., Majri-Morrison, S., Kroll, A. V., Miller, C. J., Carter, L., Goreshnik, I., Kang, A., DiMaio, F., Tarbell, K. V., and Baker, D. (2021) Computational design of a synthetic PD-1 agonist. Proc Natl Acad Sci U S A. 10.1073/pnas.2102164118
Bryan, C. M., Rocklin, G. J., Bick, M. J., Ford, A., Majri-Morrison, S., Kroll, A. V., Miller, C. J., Carter, L., Goreshnik, I., Kang, A., DiMaio, F., Tarbell, K. V., and Baker, D. (2021) Computational design of a synthetic PD-1 agonist. Proc Natl Acad Sci U S A. 10.1073/pnas.2102164118
Mulligan, V. Khipple, Kang, C. S., Sawaya, M. R., Rettie, S., Li, X., Antselovich, I., Craven, T. W., Watkins, A. M., Labonte, J. W., DiMaio, F., Yeates, T. O., and Baker, D. (2020) Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Sci. 10.1002/pro.3974
King, N. P., Sheffler, W., Sawaya, M. R., Vollmar, B. S., Sumida, J. P., André, I., Gonen, T., Yeates, T. O., and Baker, D. (2012) Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. 336, 1171-4
Danhart, E. M., Bakhtina, M., Cantara, W. A., Kuzmishin, A. B., Ma, X., Sanford, B. L., Vargas-Rodriguez, O., Košutić, M., Goto, Y., Suga, H., Nakanishi, K., Micura, R., Foster, M. P., and Musier-Forsyth, K. (2017) Conformational and chemical selection by a -acting editing domain. Proc Natl Acad Sci U S A. 114, E6774-E6783
Danhart, E. M., Bakhtina, M., Cantara, W. A., Kuzmishin, A. B., Ma, X., Sanford, B. L., Vargas-Rodriguez, O., Košutić, M., Goto, Y., Suga, H., Nakanishi, K., Micura, R., Foster, M. P., and Musier-Forsyth, K. (2017) Conformational and chemical selection by a -acting editing domain. Proc Natl Acad Sci U S A. 114, E6774-E6783
Lin, D. Yin-wei, Kueffer, L. E., Juneja, P., and Wales, T. E. (2024) Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. Elife. 10.7554/eLife.89489
Shi, K., Demir, Ö., Carpenter, M. A., Wagner, J., Kurahashi, K., Harris, R. S., Amaro, R. E., and Aihara, H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7, 17415
Wiechmann, S., Maisonneuve, P., Grebbin, B. Moyo, Hoffmeister, M., Kaulich, M., Clevers, H., Rajalingam, K., Kurinov, I., Farin, H. F., Sicheri, F., and Ernst, A. (2020) Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids. J Biol Chem. 10.1074/jbc.RA119.011025
Wiechmann, S., Maisonneuve, P., Grebbin, B. Moyo, Hoffmeister, M., Kaulich, M., Clevers, H., Rajalingam, K., Kurinov, I., Farin, H. F., Sicheri, F., and Ernst, A. (2020) Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids. J Biol Chem. 10.1074/jbc.RA119.011025
Koirala, D., Shao, Y., Koldobskaya, Y., Fuller, J. R., Watkins, A. M., Shelke, S. A., Pilipenko, E. V., Das, R., Rice, P. A., and Piccirilli, J. A. (2019) A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 10, 3629
Koirala, D., Shao, Y., Koldobskaya, Y., Fuller, J. R., Watkins, A. M., Shelke, S. A., Pilipenko, E. V., Das, R., Rice, P. A., and Piccirilli, J. A. (2019) A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 10, 3629
Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. Krishna, Nguyen, S., Davis, S. A., Rong, Y., C Middaugh, R., Weis, D. D., Dunbrack, R., Karanicolas, J., and Mantis, N. J. (2018) Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity. Protein Eng Des Sel. 10.1093/protein/gzy022
Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. Krishna, Nguyen, S., Davis, S. A., Rong, Y., C Middaugh, R., Weis, D. D., Dunbrack, R., Karanicolas, J., and Mantis, N. J. (2018) Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity. Protein Eng Des Sel. 10.1093/protein/gzy022
Xia, S., Vashishtha, A., Bulkley, D., Eom, S. Hyun, Wang, J., and Konigsberg, W. H. (2012) Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA. Biochemistry. 51, 4922-31
Robinson, R., Qureshi, I. A., Klancher, C. A., Rodriguez, P. J., Tanner, J. J., and Sobrado, P. (2015) Contribution to catalysis of ornithine binding residues in ornithine N5-monooxygenase. Arch Biochem Biophys. 585, 25-31
Da Fonseca, I., Qureshi, I. A., Mehra-Chaudhary, R., Kizjakina, K., Tanner, J. J., and Sobrado, P. (2014) Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry. 53, 7794-804
Durek, T., Torbeev, V. Yu, and Kent, S. B. H. (2007) Convergent chemical synthesis and high-resolution x-ray structure of human lysozyme. Proc Natl Acad Sci U S A. 104, 4846-51
Fetherolf, M. M., Boyd, S. D., Taylor, A. B., Kim, H. Jong, Wohlschlegel, J. A., Blackburn, N. J., P Hart, J., Winge, D. R., and Winkler, D. D. (2017) Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site. J Biol Chem. 292, 12025-12040
Almutairi, M. M., Svetlov, M. S., Hansen, D. A., Khabibullina, N. F., Klepacki, D., Kang, H. - Y., Sherman, D. H., Vázquez-Laslop, N., Polikanov, Y. S., and Mankin, A. S. (2017) Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res. 45, 9573-9582
Almutairi, M. M., Svetlov, M. S., Hansen, D. A., Khabibullina, N. F., Klepacki, D., Kang, H. - Y., Sherman, D. H., Vázquez-Laslop, N., Polikanov, Y. S., and Mankin, A. S. (2017) Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res. 45, 9573-9582
Almutairi, M. M., Svetlov, M. S., Hansen, D. A., Khabibullina, N. F., Klepacki, D., Kang, H. - Y., Sherman, D. H., Vázquez-Laslop, N., Polikanov, Y. S., and Mankin, A. S. (2017) Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res. 45, 9573-9582
Chan, A. H., Lee, W. - G., Spasov, K. A., Cisneros, J. A., Kudalkar, S. N., Petrova, Z. O., Buckingham, A. B., Anderson, K. S., and Jorgensen, W. L. (2017) Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography. Proc Natl Acad Sci U S A. 10.1073/pnas.1711463114

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