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ALS Publications by David Baker

This list is a compilation of all publications with 2024 Chemistry Nobel Laureate David Baker as co-author which used the resources of the Advanced Light Source.

Updated October 15, 2024

    1. Chevalier, B.S., T. Kortemme, M.S. Chadsey, D. Baker, R.J. Monnat, Jr., and B.L. Stoddard, “Design, Activity, and Structure of a Higly Specific Artificial Endonuclease,” Molecular Cell 10(4), 895-905 (2002). (doi:10.1016/S1097-2765(02)00690-1) 5.0.2
    2. Mcfarland, B.J., T. Kortemme, S.F. Yu, D.A. Baker, and R.K. Strong, “Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands,” Structure 11(4), 411-422 (2003). (doi:10.1016/S0969-2126(03)00047-9) 5.0.2,5.0.1
    3. Kuhlman, B., G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker, “Design of a Novel Globular Protein Fold with Atomic-Level Accuracy,” Science 302(5649), 1364-1368 (2003). (doi:10.1126/science.1089427) 8.2.1,8.2.2
      Highlight: Designing a Novel Globular Protein Fold
    4. Boulanger, M.J., A.J. Bankovich, T. Kortemme, D. Baker, and K.C. Garcia, “Convergent Mechanisms for Recognition of Divergent Cytokines by the Shared Signaling Receptor Gp130,” Molecular Cell 12(3), 577-589 (2003). (doi:10.1016/S1097-2765(03)00365-4) 5.0.2,8.2.1
    5. Kortemme, T., L.A. Joachimiak, A.N. Bullock, B.L. Stoddard, D. Baker, and A.D. Schuler, “Computational redesign of protein-protein interaction specificity,” Nature Structural & Molecular Biology 11(4), 371-379 (2004). (doi:10.1038/nsmb749) 5.0.1
    6. Korkegian, A., M.E. Black, D. Baker, and B.L. Stoddard, “Computational thermostabilization of an enzyme catalyst,” Science 308(5723), 857-860 (2005). (doi:10.1126/science.1107387) 5.0.1
    7. Joachimiak, L.A., T. Kortemme, B.L. Stoddard, and D. Baker, “Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein-Protein Interface,” Journal of Molecular Biology 361(1), 195-208 (2006). (doi:10.1016/j.jmb.2006.05.022) 5.0.3
    8. Ashworth, J., J.J. Havranek, C.M. Duarte, D. Sussman, R.J. Monnat, B.L. Stoddard, and D. Baker, “Computational redesign of endonuclease DNA binding and cleavage specificity,” Nature 441, 656-659 (2006). (doi:10.1038/nature04818) 5.0.1
    9. Dantes, G., C. Corrent, S. Reichow, J.J. Havranek, Z.M. Eletr, N.G. Isern, B. Kuhlman, G. Varani, E.A. Merritt, and D. Baker, “High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design,” Journal of Molecular Biology 366(4), 1209-1221 (2007). (doi:10.1016/j.jmb.2006.11.080) 8.2.1
    10. Sawaya, M.R., W.M. Wojtowicz, I. Andre, B. Qian, W. Wu, D. Baker, and S.L. Zipursky, “A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms,” Cell 134(6), 1007-1018 (2008). (doi:10.1016/j.cell.2008.07.042) 8.2.2
    11. McBeth, C., A. Seamons, J.C. Pizarro, S.J. Fleishman, D. Baker, T. Kortemme, J.M. Goverman, and R.K. Strong, “A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR,” Journal of Molecular Biology 375, 1306-1319 (2008). (doi:10.1016/j.jmb.2007.11.020) 5.0.1,5.0.2
    12. Spreter, T., C.K. Yip, S. Sanowar, I. Andre, T.G. Kimbrough, M. Vuckovic, W. Deng, A.C. Yu, B.B. Finlay, D. Baker, S.I. Miller, and N. Strynadka, “A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system,” Nature Structural & Molecular Biology 16(5), 468-476 (2009). (doi:10.1038/nsmb.1603) 8.2.2,8.3.1
    13. Murphy, P.M., J.M. Bolduc, J.L. Gallaher, B.L. Stoddard, and D. Baker, “Alteration of enzyme specificity by computational loop remodeling and design,” Proceedings of the National Academy of Sciences of the United States of America 106(23), 9515-9220 (2009). (doi:10.1073/pnas.0811070106) 5.0.1
    14. Siegel, J., A. Zhangellini, A. Lambert, B.L. Stoddard, and D. Baker, “Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction,” Science 329, 309-313 (2010). (doi:10.1126/science.1190239) 5.0.1
    15. Ashworth, J., G.K. Taylor, J.J. Havranek, S.A. Quadri, B.L. Stoddard, and D. Baker, “Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs,” Nucleic Acids Research 38(16), 5601-5608 (2010). (doi:10.1093/nar/gkq283) 5.0.2
    16. Azoitei, M.L., B.E. Correia, Y.A. Ban, C. Carrico, O. Kalyuzhniy, L. Chen, A. Schroeter, P. Huang, J.S. McLellan, P.D. Kwong, D. Baker, R. Strong, and W.R. Schief, “Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold,” Science 334(6054), 373-376 (2011). (doi:10.1126/science.1209368) 5.0.1
    17. Khare, S.D., Y. Kipnis, P.J. Greisen, R. Takeuchi, Y. Ashani, M. Goldsmith, Y. Song, J.L. Gallaher, I. Silman, H. Leader, J.L. Sussman, B.L. Stoddard, D.S. Tawfik, and D. Baker, “Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis,” Nature Chemical Biology 8(3), 294-300 (2012). (doi:10.1038/nchembio.777) 5.0.1
    18. Tinberg, C.E., S.D. Khare, J. Dou, L. Doyle, J.W. Nelson, A. Schena, W. Jankowski, C.G. Kalodimos, K. Johnsson, B.L. Stoddard, and D. Baker, “Computational design of ligand-binding proteins with high affinity and selectivity,” Nature 501(7466), 212-216 (2013). (doi:10.1038/nature12443) 5.0.2
    19. Procko, E., G.Y. Berguig, B.W. Shen, Y. Song, S. Frayo, A.J. Convertine, D. Margineantu, G. Booth, B.E. Correia, Y. Cheng, W.R. Schief, D.M. Hockenbery, O.W. Press, B.L. Stoddard, P.S. Stayton, and D. Baker, “A commputationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells,” Cell 157(7), 1644-1656 (2014). (doi:10.1016/j.cell.2014.04.034) 5.0.1,5.0.2
      Highlight: Designer Proteins Target Epstein-Barr-Virus-Associated Cancer
    20. Huang, P.S., G. Oberdorfer, C. Xu, X.Y. Pei, B. Nannenga, J.M. Rogers, F. DiMaio, T. Gonen, B.F. Luisi, and D. Baker, “High thermodynamic stability of parametrically designed helical bundles,” Science 346(6208), 481-485 (2014). (doi:10.1126/science.1257481) 8.2.2
    21. Correia, B.E., J.T. Bates, R.J. Loomis, G. Baneyx, C. Carrico, J.G. Jardine, P.B. Rupert, C. Correnti, O. Kalyuzhniy, V. Vittal, M.J. Connell, E. Stevens, A. Schroeter, M. Chen, S. MacPherson, A.M. Serra, Y. Adachi, M.A. Holmes, Y. Li, R.E. Klevit, B.S. Graham, R.T. Wyatt, D. Baker, R.K. Strong, J.H. Crowe, P.R. Johnson, and W.R. Schief, “Proof of principle for epitope-focused vaccine design,” Nature 507(7491), 201-206 (2014). (doi:10.1038/nature12966) 5.0.2
      Highlight: Validating Computer-Designed Proteins for Vaccines
    22. Siegel, J.B., A.L. Smith, S. Poust, A.J. Wargacki, A. Bar-Even, C. Louw, B.W. Shen, C.B. Eiben, H.M. Tran, E. Noor, J.L. Gallaher, J. Bale, Y. Yoshikuni, M.H. Gelb, J.D. Keasling, B.L. Stoddard, M.E. Lidstrom, and D. Baker, “Computational protein design enables a novel one-carbon assimilation pathway,” Proceedings of the National Academy of Sciences of the United States of America 112(12), 3704-3709 (2015). (doi:10.1073/pnas.1500545112) 5.0.1
    23. Park, K., B.W. Shen, F. Parmeggiani, P. Huang, B.L. Stoddard, and D. Baker, “Control of repeat-protein curvature by computational protein design,” Nature Structural & Molecular Biology 22(2), 167-174 (2015). (doi:10.1038/nsmb.2938) 5.0.1
    24. Doyle, L., J. Hallinan, J.M. Bolduc, F. Parmeggiani, D. Baker, B.L. Stoddard, and P. Bradley, “Rational design of α-helical tandem repeat proteins with closed architectures,” Nature 528(7583), 585-8 (2015). (doi:10.1038/nature16191) 5.0.2
    25. Brunette, T., F. Parmeggiani, P.-S. Huang, G. Bhabha, D.C. Ekiert, S.E. Tsutakawa, G.L. Hura, J.A. Tainer, and D. Baker, “Exploring the repeat protein universe through computational protein design,” Nature 528(7583), 580-4 (2015). (doi:10.1038/nature16162) 12.3.1,8.3.1
      Highlight: Exploring the Repeat-Protein Universe
    26. Smith, R., K.L. Damm-Ganamet, J.B. Dunbar, A. Ahmed, K. Chinnaswamy, J.E. Delproposto, G.M. Kubish, C. Tinberg, S.D. Khare, J. Dou, L. Doyle, J.W. Stuckey, D. Baker, and H. Carlson, “CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge,” Journal of Chemical Information and Modeling 56(6), 1022-1031 (2016). (doi:10.1021/acs.jcim.5b00387) 5.0.2
    27. Boyken, S.E., Z. Chen, B. Groves, R.A. Langan, G. Oberdorfer, A. Ford, J.M. Gilmore, C. Xu, F. DiMaio, J.H. Pereira, B. Sankaran, G. Seelig, P.H. Zwart, and D. Baker, “De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity,” Science 352(6286), 680-687 (2016). (doi:10.1126/science.aad8865) 12.3.1
      Brief: Validation of Novel Proteins Inspired by Nature
    28. Berger, S., E. Procko, D. Margineantu, E.F. Lee, B.W. Shen, A. Zelter, D.-A. Silva, K. Chawla, M.J. Herold, J.-M. Garnier, R. Johnson, M.J. MacCoss, G. Lessene, T.N. Davis, P.S. Stayton, B.L. Stoddard, W.s. Fairlie, D.M. Hockenbery, and D. Baker, “Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer,” eLife 5, e20352 (2016). (doi:10.7554/eLife.20352) 5.0.1,5.0.2,8.2.1,8.2.2
    29. Bale, J.B., S. Gonen, Y. Liu, W. Sheffler, D. Ellis, C. Thomas, D.D. Cascio, T.O. Yeates, T. Gonen, N.P. King, and D. Baker, “Accurate design of megadalton-scale two-component icosahedral protein complexes,” Science 353(6297), 389-394 (2016). (doi:10.1126/science.aaf8818) 12.3.1
      Brief: Designed Protein Nanocages Inspired by Nature
    30. Mills, J.H., W. Sheffle, M.E. Ener, P.J. Almhjell, G. Oberdorfer, J.H. Pereira, F. Parmeggiani, B. Sankaran, P.H. Zwart, and D. Baker, “Computational design of a homotrimeric metalloprotein with a trisbipyridyl core,” Proceedings of the National Academy of Sciences of the United States of America 113(52), 15012-15017 (2016). (doi:10.1073/pnas.1600188113) 8.2.1
      Brief: NCAA Drives Formation of Designed Proteins
    31. Marcos, E., B. Basanta, T.M. Chidyausiku, Y. TANG, G. Oberdorfer, G. Liu, G.T. Swapna, R. Guan, D.-A. Silva, J. Dou, J.H. Pereira, R. Xiao, B. Sankaran, P.H. Zwart, G.T. Montelione, and D. Baker, “Principles for designing proteins with cavities formed by curved β sheets,” Science 355(6321), 201-206 (2017). (doi:10.1126/science.aah7389) 8.2.1
      Highlight: Bending the (β-Sheet) Curve to Shape Protein Cavities
    32. Janda, C.Y., L.T. Dang, C. You, J. Chang, W. De Lau, Z.A. Zhong, K.S. Yan, O. Marecic, D. Siepe, X. Li, J.D. Moody, B.O. Williams, H. Clevers, J. Piehler, D. Baker, C.J. Kuo, and K.C. Garcia, “Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling,” Nature 545(7653), 234-237 (2017). (doi:10.1038/nature22306) 8.2.2
    33. Fallas, J.A., G. Ueda, W. Sheffler, V. Nguyen, D.E. McNamara, B. Sankaran, J.H. Pereira, F. Parmeggiani, T.J. Brunette, D.D. Cascio, T.O. Yeates, P.H. Zwart, and D. Baker, “Computational design of self-assembling cyclic protein homo-oligomers,” Nature Chemistry 9(4), 353-360 (2017). (doi:10.1038/nchem.2673) 8.2.1,12.3.1
      Brief: A Systematic Approach to Customizing Cyclic Proteins
    34. Dou, J., L. Doyle, P. Jr. Greisen, A. Schena, H. Park, K. Johnsson, B.L. Stoddard, and D. Baker, “Sampling and energy evaluation challenges in ligand binding protein design,” Protein Science 26(12), 2426-2437 (2017). (doi:10.1002/pro.3317) 5.0.2
    35. Chevalier, A., D.-A. Silva, G.J. Rocklin, D.R. Hicks, R. Vergara, P. Murapa, S.M. Bernard, L. Zhang, K.-H. Lam, G. Yao, C.D. Bahl, S.-I. Miyashita, I. Goreshnik, J.T. Fuller, M.T. Koday, C.M. Jenkins, T. Colvin, L. Carter, A. Bohn, C.M. Bryan, D.A. Fernández-Velasco, L. Stewart, M. Dong, X. Huang, R. Jin, I.A. Wilson, D.H. Fuller, and D. Baker, “Massively parallel de novo protein design for targeted therapeutics,” Nature 550, 74-79 (2017). (doi:10.1038/nature23912) 5.0.3
    36. Bick, M.J., P.J. Greisen, K.J. Morey, M.S. Antunes, D. La, B. Sankaran, L. Reymond, K. Johnsson, J.I. Medford, and D. Baker, “Computational design of environmental sensors for the potent opioid fentanyl,” eLife 6, e28909 (2017). (doi:10.7554/eLife.28909) 8.2.2
    37. Lu, P., D. Min, F. DiMaio, K.Y. Wei, M.D. Vahey, S.E. Boyken, Z. Chen, J.A. Fallas, G. Ueda, W. Sheffler, V.K. Mulligan, W. Xu, J.U. Bowie, and D. Baker, “Accurate computational design of multipass transmembrane proteins,” Science 359(6379), 1042-1046 (2018). (doi:10.1126/science.aaq1739) 5.0.1,8.2.1
    38. Dou, J., A.A. Vorobieva, W. Sheffler, L.A. Doyle, H. Park, M.J. Bick, B. Mao, G.W. Foight, M.Y. Lee, L.A. Gagnon, L. Carter, B. Sankaran, S. Ovchinnikov, E. Marcos, P.-S. Huang, J.C. Vaughan, B.L. Stoddard, and D. Baker, “De novo design of a fluorescence-activating β-barrel,” Nature 561(7724), 485-491 (2018). (doi:10.1038/s41586-018-0509-0) 5.0.1
    39. Silva, D.-A., S. Yu, U.Y. Ulge, J.B. Spangler, K.M. Jude, C. Labao-Almeida, L.R. Ali, A. Quijano-Rubio, M. Ruterbusch, I. Leung, T. Biary, S.J. Crowley, E. Marcos, C.D. Walkey, B.D. Weitzner, F. Pardo-Avila, J. Castellanos, L. Carter, L. Stewart, S.R. Riddell, M. Pepper, G.L. Bernardes, M. Dougan, K.C. Garcia, and D. Baker, “De novo design of potent and selective mimics of IL-2 and IL-15,” Nature 565(7738), 186-191 (2019). (doi:10.1038/s41586-018-0830-7) 5.0.1
    40. Pyles, H., S. Zhang, J.J. De Yoreo, and D. Baker, “Controlling protein assembly on inorganic crystals through designed protein interfaces,” Nature 571(7764), 251-256 (2019). (doi:10.1038/s41586-019-1361-6) 12.3.1
      Brief: Custom-Designed Models Reveal How Proteins Assemble on Minerals
    41. Mohan, K., G. Ueda, A.R. Kim, K.M. Jude, J.A. Fallas, Y. Guo, M. Hafer, Y. Miao, R. Saxton, J. Piehler, V.G. Sankaran, D. Baker, and K.C. Garcia, “Topological control of cytokine receptor signaling induces differential effects in hematopoiesis,” Science 364(6442), eaav7532 (2019). (doi:10.1126/science.aav7532) 8.2.2,5.0.1,8.2.1
    42. Langan, R.A., S.E. Boyken, A.H. Ng, J.A. Samson, G. Dods, A.M. Westbrook, T.H. Nguyen, M.J. Lajoie, Z. Chen, S. Berger, V.K. Mulligan, J.E. Dueber, W.P. Novak, H. El-Samad, and D. Baker, “De novo design of bioactive protein switches,” Nature 572(7768), 205-210 (2019). (doi:10.1038/s41586-019-1432-8) 12.3.1
    43. Koepnick, B., J. Flatten, T. Husain, A. Ford, D.-A. Silva, M.J. Bick, A. Bauer, G. Liu, Y. Ishida, A. Boykov, R.D. Estep, S. Kleinfelter, T. Norgard-Solano, L. Wei, F. Players, G.T. Montelione, F. DiMaio, Z. Popovic, F. Khatib, S. Cooper, and D. Baker, “De novo protein design by citizen scientists,” Nature 570(7761), 390-394 (2019). (doi:10.1038/s41586-019-1274-4) 5.0.2,8.2.1,8.2.2
      Highlight: A Citizen-Science Computer Game for Protein Design
    44. Foight, G.W., Z. Wang, C.T. Wei, P. Jr Greisen, K.M. Warner, D. Cunningham-Bryant, K. Park, T.J. Brunette, W. Sheffler, D. Baker, and D.J. Maly, “Multi-input chemical control of protein dimerization for programming graded cellular responses,” Nature Biotechnology 37(10), 1209-1216 (2019). (doi:10.1038/s41587-019-0242-8) 8.2.1
    45. Dang, L.T., Y. Miao, A. Ha, K. Yuki, K. Park, C.Y. Janda, K.M. Jude, K. Mohan, N.-C. Ha, M. Vallon, J. Yuan, J.G. Vilches-Moure, C.J. Kuo, K.C. Garcia, and D. Baker, “Receptor subtype discrimination using extensive shape complementary designed interfaces,” Nature Structural & Molecular Biology 26(6), 407-414 (2019). (doi:10.1038/s41594-019-0224-z) 8.2.1,8.2.2
    46. Chen, Z., M.C. Johnson, J. Chen, M.J. Bick, S.E. Boyken, B. Lin, J.J. De Yoreo, J.M. Kollman, D. Baker, and F. DiMaio, “Self-Assembling 2D Arrays with de Novo Protein Building Blocks,” Journal of the American Chemical Society 141(22), 8891-8895 (2019). (doi:10.1021/jacs.9b01978) 8.2.1
    47. Chen, Z., S.E. Boyken, M. Jia, F. Busch, D. Flores-Solis, M.J. Bick, P. Lu, Z.L. VanAernum, A. Sahasrabuddhe, R.A. Langan, S. Bermeo, T.J. Brunette, V.K. Mulligan, L.P. Carter, F. DiMaio, N.G. Sgourakis, V.H. Wysocki, and D. Baker, “Programmable design of orthogonal protein heterodimers,” Nature 565(7737), 106-111 (2019). (doi:10.1038/s41586-018-0802-y) 8.2.1,8.2.2,12.3.1
    48. Boyken, S.E., M.A. Benhaim, F. Busch, M. Jia, M.J. Bick, H. Choi, J.C. Klima, Z. Chen, C. Walkey, A. Mileant, A. Sahasrabuddhe, K.Y. Wei, E.A. Hodge, S. Byron, A. Quijano-Rubio, B. Sankaran, N.P. King, J. Lippincott-Schwartz, V.H. Wysocki, K.K. Lee, and D. Baker, “De novo design of tunable, pH-driven conformational changes,” Science 364(6441), 658-664 (2019). (doi:10.1126/science.aav7897) 8.2.2,12.3.1
    49. Xu, C., P. Lu, T.M. Gamal El-Din, X.Y. Pei, M.C. Johnson, A. Uyeda, M.J. Bick, Q. Xu, D. Jiang, H. Bai, G. Reggiano, Y. Hsia, T. Brunette, J. Dou, D. Ma, E.M. Lynch, S.E. Boyken, P.-S. Huang, L. Stewart, F. DiMaio, J.M. Kollman, B.F. Luisi, T. Matsuura, W.A. Catterall, and D. Baker, “Computational design of transmembrane pores,” Nature 585(7823), 129-134 (2020). (doi:10.1038/s41586-020-2646-5) 12.3.1,8.2.1
    50. Wei, K.Y., D. Moschidi, M.J. Bick, S. Nerli, A.C. McShan, L.P. Carter, P.-S. Huang, D.A. Fletcher, N.G. Sgourakis, S.E. Boyken, and D. Baker, “Computational design of closely related proteins that adopt two well-defined but structurally divergent folds,” Proceedings of the National Academy of Sciences of the United States of America 117(13), 7208-7215 (2020). (doi:10.1073/pnas.1914808117) 12.3.1,8.3.1,8.2.1
    51. Ueda, G., A. Antanasijevic, J.A. Fallas, W. Sheffler, J. Copps, D. Ellis, G.B. Hutchinson, A. Moyer, A. Yasmeen, Y. Tsybovsky, Y.-J. Park, M.J. Bick, B. Sankaran, R.A. Gillespie, P.J. Brouwer, P.H. Zwart, D. Veesler, M. Kanekiyo, B.S. Graham, R.W. Sanders, J.P. Moore, P.J. Klasse, A.B. Ward, N.P. King, and D. Baker, “Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens,” eLife 9, e57659 (2020). (doi:10.7554/eLife.57659) 12.3.1
    52. Lajoie, M.J., S.E. Boyken, A.I. Salter, J. Bruffey, A. Rajan, R.A. Langan, A. Olshefsky, V. Muhunthan, M.J. Bick, M. Gewe, A. Quijano-Rubio, J. Johnson, G. Lenz, A. Nguyen, S. Pun, C.E. Correnti, S.R. Riddell, and D. Baker, “Designed protein logic to target cells with precise combinations of surface antigens,” Science 369(6511), 1637-1643 (2020). (doi:10.1126/science.aba6527) 8.2.2
    53. Chen, Z., R.D. Kibler, A. Hunt, F. Busch, J. Pearl, M. Jia, Z.L. VanAernum, B.M. Wicky, G. Dods, H. Liao, M.S. Wilken, C. Ciarlo, S. Green, H. El-Samad, J. Stamatoyannopoulos, V.H. Wysocki, M.C. Jewett, S.E. Boyken, and D. Baker, “De novo design of protein logic gates,” Science 368(6486), 78-84 (2020). (doi:10.1126/science.aay2790) 12.3.1
    54. Brunette, T., M.J. Bick, J.M. Hansen, C.M. Chow, J.M. Kollman, and D. Baker, “Modular repeat protein sculpting using rigid helical junctions,” Proceedings of the National Academy of Sciences of the United States of America 117(16), 8870-8875 (2020). (doi:10.1073/pnas.1908768117) 12.3.1
    55. Basanta, B., M.J. Bick, A.K. Bera, C. Norn, C.M. Chow, L.P. Carter, I. Goreshnik, F. Dimaio, and D. Baker, “An enumerative algorithm for de novo design of proteins with diverse pocket structures,” Proceedings of the National Academy of Sciences of the United States of America 117(36), 22135-22145 (2020). (doi:10.1073/pnas.2005412117) 8.2.1,8.2.2
    56. Woodall, N.B., Z. Weinberg, J. Park, F. Busch, R.S. Johnson, M.J. Feldbauer, M. Murphy, M. Ahlrichs, I. Yousif, M.J. MacCoss, V.H. Wysocki, H. El-Samad, and D. Baker, “De novo design of tyrosine and serine kinase-driven protein switches,” Nature Structural & Molecular Biology 28(9), 762-770 (2021). (doi:10.1038/s41594-021-00649-8) 12.3.1
    57. Vulovic, I., Q. Yao, Y.-J. Park, A. Courbet, A. Norris, F. Busch, A. Sahasrabuddhe, H. Merten, D.D. Sahtoe, G. Ueda, J.A. Fallas, S.J. Weaver, Y. Hsia, R.A. Langan, A. Plückthun, V.H. Wysocki, D. Veesler, G.J. Jensen, and D. Baker, “Generation of ordered protein assemblies using rigid three-body fusion,” Proceedings of the National Academy of Sciences of the United States of America 118(23), e201503711 (2021). (doi:10.1073/pnas.2015037118) 12.3.1
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      Highlight: Computer-Aided Protein Design for New Biomaterials
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