Barry L. Stoddard - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
General Biophysics, Biochemistry

156 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, ... ... Stoddard BL, et al. De novo design of a fluorescence-activating β-barrel. Nature. PMID 30209393 DOI: 10.1038/s41586-018-0509-0  0.32
2017 Dou J, Doyle L, Greisen PJ, Schena A, Park H, Johnsson K, Stoddard BL, Baker D. Sampling and Energy Evaluation Challenges in Ligand Binding Protein Design. Protein Science : a Publication of the Protein Society. PMID 28980354 DOI: 10.1002/pro.3317  0.32
2017 Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Engineering, Design & Selection : Peds. 30: 503-522. PMID 28873986 DOI: 10.1093/protein/gzx037  0.4
2017 Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL. Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity. Nucleic Acids Research. PMID 28637173 DOI: 10.1093/nar/gkx544  0.4
2016 Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, ... Stoddard BL, et al. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 5. PMID 27805565 DOI: 10.7554/eLife.20352  0.32
2016 Stoddard BL, Fox K. Editorial: CRISPR in Nucleic Acids Research. Nucleic Acids Research. 44: 4989-90. PMID 27325109 DOI: 10.1093/nar/gkw451  1
2016 Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL. Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure (London, England : 1993). PMID 27133026 DOI: 10.1016/j.str.2016.03.024  1
2015 Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK. The structural basis of asymmetry in DNA binding and cleavage as exhibited by the I-SmaMI LAGLIDADG meganuclease. Journal of Molecular Biology. PMID 26705195 DOI: 10.1016/j.jmb.2015.12.005  1
2015 Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. Rational design of α-helical tandem repeat proteins with closed architectures. Nature. PMID 26675735 DOI: 10.1038/nature16191  1
2015 King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife. 4. PMID 26650357 DOI: 10.7554/eLife.11012  1
2015 Jeltsch A, Wende W, Friedhoff P, Stoddard BL. Editorial: Alfred Pingoud (1945-2015). Nucleic Acids Research. 43: 7661-3. PMID 26385498 DOI: 10.1093/nar/gkv846  1
2015 Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, ... Stoddard BL, et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences of the United States of America. 112: 3704-9. PMID 25775555 DOI: 10.1073/pnas.1500545112  1
2015 Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology. 22: 167-74. PMID 25580576 DOI: 10.1038/nsmb.2938  1
2015 Takeuchi R, Choi M, Stoddard BL. Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization. Methods in Molecular Biology (Clifton, N.J.). 1239: 105-32. PMID 25408403 DOI: 10.1007/978-1-4939-1862-1_6  1
2014 Corey DR, Wise JA, Fox KR, Stoddard BL. Breakthrough articles: putting science first. Nucleic Acids Research. 42: 11273-4. PMID 25301802 DOI: 10.1093/nar/gku853  1
2014 Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell. 157: 1644-56. PMID 24949974 DOI: 10.1016/j.cell.2014.04.034  1
2014 Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, Stoddard BL, Windbichler N, Crisanti A. A synthetic sex ratio distortion system for the control of the human malaria mosquito. Nature Communications. 5: 3977. PMID 24915045 DOI: 10.1038/ncomms4977  1
2014 Takeuchi R, Choi M, Stoddard BL. Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proceedings of the National Academy of Sciences of the United States of America. 111: 4061-6. PMID 24591643 DOI: 10.1073/pnas.1321030111  1
2014 Stoddard BL. Homing endonucleases from mobile group I introns: discovery to genome engineering. Mobile Dna. 5: 7. PMID 24589358 DOI: 10.1186/1759-8753-5-7  1
2014 Zhao L, Stoddard BL. Rapid determination of homing endonuclease DNA binding specificity profile. Methods in Molecular Biology (Clifton, N.J.). 1123: 127-34. PMID 24510265 DOI: 10.1007/978-1-62703-968-0_10  1
2014 Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. MegaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering Nucleic Acids Research. 42: 2591-2601. PMID 24285304 DOI: 10.1093/nar/gkt1224  1
2013 Chan YS, Takeuchi R, Jarjour J, Huen DS, Stoddard BL, Russell S. The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive. Plos One. 8: e74254. PMID 24040217 DOI: 10.1371/journal.pone.0074254  1
2013 Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 501: 212-6. PMID 24005320 DOI: 10.1038/nature12443  1
2013 Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal of the American Chemical Society. 135: 13393-9. PMID 23924187 DOI: 10.1021/ja403503m  1
2013 Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends in Cell Biology. 23: 390-8. PMID 23707478 DOI: 10.1016/j.tcb.2013.04.003  1
2013 Metzger MJ, Stoddard BL, Monnat RJ. PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks. Dna Repair. 12: 529-34. PMID 23684799 DOI: 10.1016/j.dnarep.2013.04.004  1
2013 Mak AN, Bradley P, Bogdanove AJ, Stoddard BL. TAL effectors: function, structure, engineering and applications. Current Opinion in Structural Biology. 23: 93-9. PMID 23265998 DOI: 10.1016/j.sbi.2012.11.001  1
2012 Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J, Baker D, Stoddard BL, Scharenberg AM. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Research. 40: 7985-8000. PMID 22684507 DOI: 10.1093/nar/gks502  1
2012 Taylor GK, Petrucci LH, Lambert AR, Baxter SK, Jarjour J, Stoddard BL. LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Research. 40: W110-6. PMID 22570419 DOI: 10.1093/nar/gks365  1
2012 Taylor GK, Stoddard BL. Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms. Nucleic Acids Research. 40: 5189-200. PMID 22406833 DOI: 10.1093/nar/gks226  1
2012 Jacoby K, Metzger M, Shen BW, Certo MT, Jarjour J, Stoddard BL, Scharenberg AM. Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space. Nucleic Acids Research. 40: 4954-64. PMID 22334611 DOI: 10.1093/nar/gkr1303  1
2012 Khare SD, Kipnis Y, Greisen P, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology. 8: 294-300. PMID 22306579 DOI: 10.1038/nchembio.777  1
2012 Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology. 30: 190-2. PMID 22267011 DOI: 10.1038/nbt.2109  1
2012 Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science (New York, N.Y.). 335: 716-9. PMID 22223736 DOI: 10.1126/science.1216211  1
2011 Kaiser BK, Stoddard BL. DNA recognition and transcriptional regulation by the WhiA sporulation factor. Scientific Reports. 1: 156. PMID 22355671 DOI: 10.1038/srep00156  1
2011 Taylor GK, Heiter DF, Pietrokovski S, Stoddard BL. Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. Nucleic Acids Research. 39: 9705-19. PMID 21890897 DOI: 10.1093/nar/gkr669  1
2011 Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL. Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proceedings of the National Academy of Sciences of the United States of America. 108: 13077-82. PMID 21784983 DOI: 10.1073/pnas.1107719108  1
2011 Shen BW, Xu D, Chan SH, Zheng Y, Zhu Z, Xu SY, Stoddard BL. Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI. Nucleic Acids Research. 39: 8223-36. PMID 21724614 DOI: 10.1093/nar/gkr543  1
2011 Stoddard BL. Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure (London, England : 1993). 19: 7-15. PMID 21220111 DOI: 10.1016/j.str.2010.12.003  1
2011 Metzger MJ, McConnell-Smith A, Stoddard BL, Miller AD. Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template. Nucleic Acids Research. 39: 926-35. PMID 20876694 DOI: 10.1093/nar/gkq826  1
2011 Chan SH, Stoddard BL, Xu SY. Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Research. 39: 1-18. PMID 20805246 DOI: 10.1093/nar/gkq742  1
2010 Mak AN, Lambert AR, Stoddard BL. Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI. Structure (London, England : 1993). 18: 1321-31. PMID 20800503 DOI: 10.1016/j.str.2010.07.006  1
2010 Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science (New York, N.Y.). 329: 309-13. PMID 20647463 DOI: 10.1126/science.1190239  1
2010 Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL. Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure (London, England : 1993). 18: 734-43. PMID 20541511 DOI: 10.1016/j.str.2010.03.009  1
2010 Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research. 38: 5601-8. PMID 20435674 DOI: 10.1093/nar/gkq283  1
2009 Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 461: 1300-4. PMID 19865174 DOI: 10.1038/nature08508  1
2009 Kaiser BK, Clifton MC, Shen BW, Stoddard BL. The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Structure (London, England : 1993). 17: 1368-76. PMID 19836336 DOI: 10.1016/j.str.2009.08.008  1
2009 Jarjour J, West-Foyle H, Certo MT, Hubert CG, Doyle L, Getz MM, Stoddard BL, Scharenberg AM. High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Research. 37: 6871-80. PMID 19740766 DOI: 10.1093/nar/gkp726  1
2009 Fuchita M, Ardiani A, Zhao L, Serve K, Stoddard BL, Black ME. Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo. Cancer Research. 69: 4791-9. PMID 19487291 DOI: 10.1158/0008-5472.CAN-09-0615  1
2009 Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D. Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106: 9215-20. PMID 19470646 DOI: 10.1073/pnas.0811070106  1
2009 McConnell Smith A, Takeuchi R, Pellenz S, Davis L, Maizels N, Monnat RJ, Stoddard BL. Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proceedings of the National Academy of Sciences of the United States of America. 106: 5099-104. PMID 19276110 DOI: 10.1073/pnas.0810588106  1
2009 Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S. Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Research. 37: 2560-73. PMID 19264795 DOI: 10.1093/nar/gkp095  1
2009 Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ. Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins. Nucleic Acids Research. 37: 1650-62. PMID 19153140 DOI: 10.1093/nar/gkp004  1
2009 Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL. Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Research. 37: 877-90. PMID 19103658 DOI: 10.1093/nar/gkn1007  1
2009 Zhao L, Pellenz S, Stoddard BL. Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I. Journal of Molecular Biology. 385: 1498-510. PMID 19038269 DOI: 10.1016/j.jmb.2008.10.096  1
2008 Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL. Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases. Nucleic Acids Research. 36: 6988-98. PMID 18984620 DOI: 10.1093/nar/gkn846  1
2008 Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL. Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure (London, England : 1993). 16: 558-69. PMID 18400177 DOI: 10.1016/j.str.2008.01.017  1
2008 Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D. De novo computational design of retro-aldol enzymes. Science (New York, N.Y.). 319: 1387-91. PMID 18323453 DOI: 10.1126/science.1152692  1
2008 Stolworthy TS, Korkegian AM, Willmon CL, Ardiani A, Cundiff J, Stoddard BL, Black ME. Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine. Journal of Molecular Biology. 377: 854-69. PMID 18291415 DOI: 10.1016/j.jmb.2008.01.002  1
2008 Shen BW, Spiegel PC, Chang CH, Huh JW, Lee JS, Kim J, Kim YH, Stoddard BL. The tertiary structure and domain organization of coagulation factor VIII. Blood. 111: 1240-7. PMID 17965321 DOI: 10.1182/blood-2007-08-109918  1
2007 Eastberg JH, McConnell Smith A, Zhao L, Ashworth J, Shen BW, Stoddard BL. Thermodynamics of DNA target site recognition by homing endonucleases. Nucleic Acids Research. 35: 7209-21. PMID 17947319 DOI: 10.1093/nar/gkm867  1
2007 Scalley-Kim M, McConnell-Smith A, Stoddard BL. Coevolution of a homing endonuclease and its host target sequence. Journal of Molecular Biology. 372: 1305-19. PMID 17720189 DOI: 10.1016/j.jmb.2007.07.052  1
2007 Eastberg JH, Eklund J, Monnat R, Stoddard BL. Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry. 46: 7215-25. PMID 17516660 DOI: 10.1021/bi700418d  1
2007 Volná P, Jarjour J, Baxter S, Roffler SR, Monnat RJ, Stoddard BL, Scharenberg AM. Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases. Nucleic Acids Research. 35: 2748-58. PMID 17426121 DOI: 10.1093/nar/gkm182  1
2007 Zhao L, Bonocora RP, Shub DA, Stoddard BL. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. The Embo Journal. 26: 2432-42. PMID 17410205 DOI: 10.1038/sj.emboj.7601672  1
2006 Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM. Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Research. 34: 4791-800. PMID 16971456 DOI: 10.1093/nar/gkl645  1
2006 Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/j.jmb.2006.07.092  1
2006 Joachimiak LA, Kortemme T, Stoddard BL, Baker D. 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: 195-208. PMID 16831445 DOI: 10.1016/j.jmb.2006.05.022  1
2006 Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441: 656-9. PMID 16738662 DOI: 10.1038/nature04818  1
2006 Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux C, Stoddard BL. The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure (London, England : 1993). 14: 869-80. PMID 16698548 DOI: 10.1016/j.str.2006.03.009  1
2006 Landthaler M, Shen BW, Stoddard BL, Shub DA. I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities. Journal of Molecular Biology. 358: 1137-51. PMID 16569414 DOI: 10.1016/j.jmb.2006.02.054  1
2005 Stoddard BL. Homing endonuclease structure and function. Quarterly Reviews of Biophysics. 38: 49-95. PMID 16336743 DOI: 10.1017/S0033583505004063  1
2005 Korkegian A, Black ME, Baker D, Stoddard BL. Computational thermostabilization of an enzyme. Science (New York, N.Y.). 308: 857-60. PMID 15879217 DOI: 10.1126/science.1107387  1
2005 Perraud AL, Takanishi CL, Shen B, Kang S, Smith MK, Schmitz C, Knowles HM, Ferraris D, Li W, Zhang J, Stoddard BL, Scharenberg AM. Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels. The Journal of Biological Chemistry. 280: 6138-48. PMID 15561722 DOI: 10.1074/jbc.M411446200  1
2004 Chevalier B, Sussman D, Otis C, Noël AJ, Turmel M, Lemieux C, Stephens K, Monnat RJ, Stoddard BL. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry. 43: 14015-26. PMID 15518550 DOI: 10.1021/bi048970c  1
2004 Spiegel PC, Kaiser SM, Simon JA, Stoddard BL. Disruption of protein-membrane binding and identification of small-molecule inhibitors of coagulation factor VIII. Chemistry & Biology. 11: 1413-22. PMID 15489168 DOI: 10.1016/j.chembiol.2004.08.006  1
2004 Spiegel PC, Murphy P, Stoddard BL. Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities. The Journal of Biological Chemistry. 279: 53691-8. PMID 15471879 DOI: 10.1074/jbc.M409389200  1
2004 Mahan SD, Ireton GC, Knoeber C, Stoddard BL, Black ME. Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Protein Engineering, Design & Selection : Peds. 17: 625-33. PMID 15381761 DOI: 10.1093/protein/gzh074  1
2004 Shen BW, Landthaler M, Shub DA, Stoddard BL. DNA binding and cleavage by the HNH homing endonuclease I-HmuI. Journal of Molecular Biology. 342: 43-56. PMID 15313606 DOI: 10.1016/j.jmb.2004.07.032  1
2004 Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Stoddard BL, Seligman LM. Isolation and characterization of new homing endonuclease specificities at individual target site positions. Journal of Molecular Biology. 342: 31-41. PMID 15313605 DOI: 10.1016/j.jmb.2004.07.031  1
2004 Mahan SD, Ireton GC, Stoddard BL, Black ME. Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference. Biochemistry. 43: 8957-64. PMID 15248753 DOI: 10.1021/bi049720z  1
2004 Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nature Structural & Molecular Biology. 11: 371-9. PMID 15034550 DOI: 10.1038/nsmb749  1
2004 Bakhrat A, Jurica MS, Stoddard BL, Raveh D. Homology modeling and mutational analysis of Ho endonuclease of yeast. Genetics. 166: 721-8. PMID 15020462 DOI: 10.1534/genetics.166.2.721  1
2004 Ireton GC, Stoddard BL. Microseed matrix screening to improve crystals of yeast cytosine deaminase. Acta Crystallographica. Section D, Biological Crystallography. 60: 601-5. PMID 14993707 DOI: 10.1107/S0907444903029664  1
2004 Eastberg JH, Pelletier J, Stoddard BL. Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Nucleic Acids Research. 32: 653-60. PMID 14754987 DOI: 10.1093/nar/gkh212  1
2003 Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL. Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes & Development. 17: 2875-88. PMID 14633971 DOI: 10.1101/gad.1109003  1
2003 Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science (New York, N.Y.). 302: 1364-8. PMID 14631033 DOI: 10.1126/science.1089427  1
2003 Shen BW, Perraud AL, Scharenberg A, Stoddard BL. The crystal structure and mutational analysis of human NUDT9. Journal of Molecular Biology. 332: 385-98. PMID 12948489 DOI: 10.1016/S0022-2836(03)00954-9  1
2003 Ireton GC, Black ME, Stoddard BL. The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure (London, England : 1993). 11: 961-72. PMID 12906827 DOI: 10.1016/S0969-2126(03)00153-9  1
2003 Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL. Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. Journal of Molecular Biology. 329: 253-69. PMID 12758074 DOI: 10.1016/S0022-2836(03)00447-9  1
2003 Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, ... ... Stoddard BL, et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Research. 31: 1805-12. PMID 12654995 DOI: 10.1093/nar/gkg274  1
2003 Perraud AL, Shen B, Dunn CA, Rippe K, Smith MK, Bessman MJ, Stoddard BL, Scharenberg AM. NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase. The Journal of Biological Chemistry. 278: 1794-801. PMID 12427752 DOI: 10.1074/jbc.M205601200  1
2002 Galburt EA, Stoddard BL. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry. 41: 13851-60. PMID 12437341 DOI: 10.1021/bi020467h  1
2002 Stoddard BL. Nuclease enzymes. Methods (San Diego, Calif.). 28: 301. PMID 12431433 DOI: 10.1016/S1046-2023(02)00236-0  1
2002 Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Molecular Cell. 10: 895-905. PMID 12419232 DOI: 10.1016/S1097-2765(02)00690-1  1
2002 Spiegel PC, Stoddard BL. Optimization of factor VIII replacement therapy: can structural studies help in evading antibody inhibitors? British Journal of Haematology. 119: 310-22. PMID 12406063 DOI: 10.1046/j.1365-2141.2002.03845.x  1
2002 Galburt EA, Pelletier J, Wilson G, Stoddard BL. Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure (London, England : 1993). 10: 1249-60. PMID 12220496 DOI: 10.1016/S0969-2126(02)00835-3  1
2002 Ireton GC, McDermott G, Black ME, Stoddard BL. The structure of Escherichia coli cytosine deaminase. Journal of Molecular Biology. 315: 687-97. PMID 11812140 DOI: 10.1006/jmbi.2001.5277  1
2001 Ireton GC, Black ME, Stoddard BL. Crystallization and preliminary X-ray analysis of bacterial cytosine deaminase. Acta Crystallographica. Section D, Biological Crystallography. 57: 1643-5. PMID 11679731 DOI: 10.1107/S0907444901011064  1
2001 Chevalier BS, Stoddard BL. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Research. 29: 3757-74. PMID 11557808  1
2001 Spiegel PC, Jacquemin M, Saint-Remy JM, Stoddard BL, Pratt KP. Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII. Blood. 98: 13-9. PMID 11418455 DOI: 10.1182/blood.V98.1.13  1
2001 Stoddard BL. Trapping reaction intermediates in macromolecular crystals for structural analyses. Methods (San Diego, Calif.). 24: 125-38. PMID 11384188 DOI: 10.1006/meth.2001.1174  1
2001 Chevalier BS, Monnat RJ, Stoddard BL. The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nature Structural Biology. 8: 312-6. PMID 11276249 DOI: 10.1038/86181  1
2001 Galburt EA, Stoddard BL. Time-resolved macromolecular crystallography Physics Today. 54: 33-39.  1
2000 Bond CJ, Jurica MS, Mesecar A, Stoddard BL. Determinants of allosteric activation of yeast pyruvate kinase and identification of novel effectors using computational screening Biochemistry. 39: 15333-15343. PMID 11112519 DOI: 10.1021/bi001443i  1
2000 Bond CJ, Huang J, Hajduk R, Flick KE, Heath PJ, Stoddard BL. Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis Acta Crystallographica Section D: Biological Crystallography. 56: 1359-1366. PMID 11053832 DOI: 10.1107/S0907444900009537  1
2000 Liu ML, Shen BW, Nakaya S, Pratt KP, Fujikawa K, Davie EW, Stoddard BL, Thompson AR. Hemophilic factor VIII C1- and C2-domain missense mutations and their modeling to the 1.5-angstrom human C2-domain crystal structure. Blood. 96: 979-87. PMID 10910913  1
2000 Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ, Stoddard BL. Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site. Journal of Molecular Biology. 300: 877-87. PMID 10891275 DOI: 10.1006/jmbi.2000.3874  1
2000 Galburt EA, Stoddard BL. Restriction endonucleases: one of these things is not like the others. Nature Structural Biology. 7: 89-91. PMID 10655603 DOI: 10.1038/72450  1
1999 Pratt KP, Shen BW, Takeshima K, Davie EW, Fujikawa K, Stoddard BL. Structure of the C2 domain of human factor VIII at 1.5 A resolution. Nature. 402: 439-42. PMID 10586887 DOI: 10.1038/46601  1
1999 Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ, Stoddard BL. A novel endonuclease mechanism directly visualized for I-PpoI. Nature Structural Biology. 6: 1096-9. PMID 10581547 DOI: 10.1038/70027  1
1999 Jurica MS, Stoddard BL. Homing endonucleases: Structure, function and evolution Cellular and Molecular Life Sciences. 55: 1304-1326. PMID 10487208 DOI: 10.1007/s000180050372  1
1999 Shen BW, Dyer DH, Huang JY, D'Ari L, Rabinowitz J, Stoddard BL. The crystal structure of a bacterial, bifunctional 5,10 methylene- tetrahydrofolate dehydrogenase/cyclohydrolase Protein Science. 8: 1342-1349. PMID 10386884  1
1999 Bryant MD, Flick KE, Koduri RS, Wilton DC, Stoddard BL, Gelb MH. 1,3-Dioxane-4,6-dione-5-carboxamide-based inhibitors of human group IIA phospholipase A: X-ray structure of the complex and interfacial selection of inhibitors from a structural library. Bioorganic & Medicinal Chemistry Letters. 9: 1097-102. PMID 10328292 DOI: 10.1016/S0960-894X(99)00147-X  1
1999 Stoddard BL. Visualizing enzyme intermediates using fast diffraction and reaction trapping methods: Isocitrate dehydrogenase Biochemical Society Transactions. 27: 42-48. PMID 10093704  1
1999 Ren Z, Bourgeois D, Helliwell JR, Moffat K, Šrajer V, Stoddard BL. Laue crystallography: Coming of age Journal of Synchrotron Radiation. 6: 891-917.  1
1998 Stoddard BL. New results using Laue diffraction and time-resolved crystallography Current Opinion in Structural Biology. 8: 612-618. PMID 9818266 DOI: 10.1016/S0959-440X(98)80153-X  1
1998 Jurica MS, Monnat RJ, Stoddard BL. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-Crel Molecular Cell. 2: 469-476. PMID 9809068  1
1998 Stoddard BL, Cohen BE, Brubaker M, Mesecar AD, Koshland DE. Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs. Nature Structural Biology. 5: 891-7. PMID 9783749 DOI: 10.1038/2331  1
1998 Jurica MS, Stoddard BL. Mind your B's and R's: Bacterial chemotaxis, signal transduction and protein recognition Structure. 6: 809-813. PMID 9687374  1
1998 Flick KE, Jurica MS, Monnat RJ, Stoddard BL. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-Ppol Nature. 394: 96-101. PMID 9665136 DOI: 10.1038/27952  1
1998 Jurica MS, Mesecar A, Heath PJ, Shi W, Nowak T, Stoddard BL. The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate Structure. 6: 195-210. PMID 9519410  1
1998 Stoddard BL, Pietrokovski S. Breaking up is hard to do Nature Structural Biology. 5: 3-5. PMID 9437416 DOI: 10.1038/nsb0198-3  1
1998 Stoddard BL, Bolduc JM, Dyer DH, Scott WG, Sweet RM. Visualizing enzyme and ribozyme intermediates using fast diffraction and reaction trapping methods Pure and Applied Chemistry. 70: 17-23.  1
1997 Flick KE, McHugh D, Heath JD, Stephens KM, Monnat RJ, Stoddard BL. Crystallization and preliminary X-ray studies of I-PpoI: a nuclear, intron-encoded homing endonuclease from Physarum polycephalum. Protein Science : a Publication of the Protein Society. 6: 2677-80. PMID 9416623 DOI: 10.1002/pro.5560061226  1
1997 Cohen BE, Stoddard BL, Koshland DE. Caged NADP and NAD. Synthesis and characterization of functionally distinct caged compounds Biochemistry. 36: 9035-9044. PMID 9220992 DOI: 10.1021/bi970263e  1
1997 Mesecar AD, Stoddard BL, Koshland DE. Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Science (New York, N.Y.). 277: 202-6. PMID 9211842 DOI: 10.1126/science.277.5323.202  1
1997 Heath PJ, Stephens KM, Monnat RJ, Stoddard BL. The structure of I-CreI, a group I intron-encoded homing endonuclease Nature Structural Biology. 4: 468-476. PMID 9187655 DOI: 10.1038/nsb0697-468  1
1997 Stephens KM, Monnat RJ, Heath PJ, Stoddard BL. Crystallization and preliminary X-ray studies of I-CreI: A group I intron-encoded endonuclease from C. reinhardtii Proteins: Structure, Function and Genetics. 28: 137-139. PMID 9144800 DOI: 10.1002/(SICI)1097-0134(199705)28:1<137::AID-PROT15>3.0.CO;2-K  1
1997 Cheung E, D'Ari L, Rabinowitz JC, Dyer DH, Huang JY, Stoddard BL. Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene-tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli. Proteins. 27: 322-4. PMID 9061797 DOI: 10.1002/(SICI)1097-0134(199702)27:2<322::AID-PROT19>3.0.CO;2-O  1
1997 D'Ari L, Cheung E, Rabinowitz JC, Bolduc JM, Huang JY, Stoddard BL. Purification, crystallization, and preliminary X-ray studies of 10-formyltetrahydrofolate synthetase from Clostridia acidici-urici. Proteins. 27: 319-21. PMID 9061796 DOI: 10.1002/(SICI)1097-0134(199702)27:2<319::AID-PROT18>3.0.CO;2-P  1
1997 Mesecar AD, Stoddard BL, Koshtand DE. Small conformational changes of an enzyme under catalytic turnover-the isocitrate dehydrogenase catalyzed reaction Faseb Journal. 11: A1314.  1
1996 Stoddard BL, Flickt KE. Calcineurin-immunosuppressor complexes Current Opinion in Structural Biology. 6: 770-775. PMID 8994877 DOI: 10.1016/S0959-440X(96)80006-6  1
1996 Scott WG, Murray JB, Arnold JR, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science (New York, N.Y.). 274: 2065-9. PMID 8953035 DOI: 10.1126/science.274.5295.2065  1
1996 Stoddard BL. Caught in a chemical trap Nature Structural Biology. 3: 907-909. PMID 8901863 DOI: 10.1038/nsb1196-907  1
1996 Stoddard BL. Intermediate trapping and Laue X-ray diffraction: Potential for enzyme mechanism, dynamics, and inhibitor screening Pharmacology and Therapeutics. 70: 215-256. PMID 8888067 DOI: 10.1016/0163-7258(96)00058-7  1
1996 Stoddard BL, Dean A, Bash PA. Combining Laue diffraction and molecular dynamics to study enzyme intermediates Nature Structural Biology. 3: 590-595. PMID 8673602 DOI: 10.1038/nsb0796-590  1
1995 Stoddard BL, Farber GK. Direct measurement of reactivity in the protein crystal by steady-state kinetic studies Structure. 3: 991-996. PMID 8590009 DOI: 10.1016/S0969-2126(01)00235-0  1
1995 Bolduc JM, Dyer DH, Scott WG, Singer P, Sweet RM, Koshland DE, Stoddard BL. Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Science (New York, N.Y.). 268: 1312-8. PMID 7761851  1
1994 Scott WG, Stoddard BL. Transmembrane signalling and the aspartate receptor Structure. 2: 877-887. PMID 7812719 DOI: 10.1016/S0969-2126(94)00088-3  1
1993 Stoddard BL, Koshland DE. Molecular recognition analyzed by docking simulations: The aspartate receptor and isocitrate dehydrogenase from Escherichia coli Proceedings of the National Academy of Sciences of the United States of America. 90: 1146-1153. PMID 8433976 DOI: 10.1073/pnas.90.4.1146  1
1993 Stoddard BL, Koshland DE. Structure of isocitrate dehydrogenase with α-ketoglutarate at 2.7-å resolution: conformational changes induced by decarboxylation of isocitrate Biochemistry®. 32: 9317-9322. PMID 8369301  1
1993 Stoddard BL, Dean A, Koshland DE. Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-å resolution: a pseudo-michaelis ternary complex Biochemistry®. 32: 9310-9316. PMID 8369300  1
1993 Stoddard BL, Farber GK, Strong RK. The facts and fancy of microgravity protein crystallization Biotechnology and Genetic Engineering Reviews. 11: 57-77. PMID 7840848 DOI: 10.1080/02648725.1993.10647898  1
1992 Stoddard BL, Bui JD, Koshland DE. Structure and dynamics of transmembrane signaling by the Escherichia coli aspartate receptor. Biochemistry. 31: 11978-83. PMID 1457398  1
1992 Stoddard BL, Strong RK, Arrott A, Farber GK. Mir for the crystallographers' money Nature. 360: 293-294. PMID 1448142  1
1992 Stoddard BL, Biemann HP, Koshland DE. Receptors and transmembrane signaling Cold Spring Harbor Symposia On Quantitative Biology. 57: 1-16. PMID 1339648  1
1992 Stoddard BL, Koshland DE. Prediction of the structure of a receptor-protein complex using a binary docking method Nature. 358: 774-776. PMID 1324436  1
1992 Strong RK, Stoddard BL, Arrott A, Farber GK. Long duration growth of protein crystals in microgravity aboard the MIR space station Journal of Crystal Growth. 119: 200-214. DOI: 10.1016/0022-0248(92)90672-6  1
1991 Stoddard BL, Koenigs P, Porter N, Petratos K, Petsko GA, Ringe D. Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography Proceedings of the National Academy of Sciences of the United States of America. 88: 5503-5507. PMID 2062832  1
1991 Stoddard BL, Strong RK, Farber GK, Arrott A, Petsko GA. Design of apparatus and experiments to determine the effect of microgravity on the crystallization of biological macromolecules using the MIR spacestation Journal of Crystal Growth. 110: 312-316. DOI: 10.1016/0022-0248(91)90900-P  1
1990 Stoddard BL, Bruhnke J, Porter N, Ringe D, Petsko GA. Structure and activity of two photoreversible cinnamates bound to chymotrypsin Biochemistry. 29: 4871-4879. PMID 2364065 DOI: 10.1021/bi00472a017  1
1990 Stoddard BL, Lynne Howell P, Ringe D, Petsko GA. The 2.1-Å resolution structure of iron superoxide dismutase from Pseudomonas ovalis Biochemistry®. 29: 8885-8893. PMID 2271564  1
1990 Stoddard BL, Bruhnke J, Koenigs P, Porter N, Ringe D, Petsko GA. Photolysis and deacylation of inhibited chymotrypsin Biochemistry. 29: 8042-8051. PMID 2261462  1
1990 Stoddard BL, Ringe D, Petsko GA. The structure of iron superoxide dismutase from Pseudomonas ovalis complexed with the inhibitor azide Protein Engineering, Design and Selection. 4: 113-119. PMID 2075185 DOI: 10.1093/protein/4.2.113  1
1987 Connolly DT, Stoddard BL, Harakas NK, Feder J. Human fibroblast-derived growth factor is a mitogen and chemoattractant for endothelial cells Biochemical and Biophysical Research Communications. 144: 705-712. PMID 3579937 DOI: 10.1016/S0006-291X(87)80022-0  1
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