| Year |
Citation |
Score |
| 2023 |
Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, ... ... Stoddard BL, et al. Computational design of sequence-specific DNA-binding proteins. Biorxiv : the Preprint Server For Biology. PMID 37790440 DOI: 10.1101/2023.09.20.558720 |
0.346 |
|
| 2023 |
Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL. Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI. Nucleic Acids Research. PMID 36987874 DOI: 10.1093/nar/gkad228 |
0.396 |
|
| 2023 |
Shen BW, Doyle LA, Werther R, Westburg AA, Bies DP, Walter SI, Luyten YA, Morgan RD, Stoddard BL, Kaiser BK. Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor. Nucleic Acids Research. PMID 36794719 DOI: 10.1093/nar/gkad083 |
0.404 |
|
| 2022 |
Luyten YA, Hausman DE, Young JC, Doyle LA, Higashi KM, Ubilla-Rodriguez NC, Lambert AR, Arroyo CS, Forsberg KJ, Morgan RD, Stoddard BL, Kaiser BK. Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Research. PMID 35511079 DOI: 10.1093/nar/gkac311 |
0.753 |
|
| 2021 |
Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL, Kaiser BK, Malik HS. The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity. Plos Biology. 19: e3001428. PMID 34644300 DOI: 10.1371/journal.pbio.3001428 |
0.301 |
|
| 2021 |
Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL. Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Structure (London, England : 1993). PMID 33826880 DOI: 10.1016/j.str.2021.03.012 |
0.401 |
|
| 2020 |
Lambert AR, Hallinan JP, Werther R, Głów D, Stoddard BL. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Structure (London, England : 1993). PMID 32359399 DOI: 10.1016/J.Str.2020.04.009 |
0.779 |
|
| 2020 |
Correnti CE, Hallinan JP, Doyle LA, Ruff RO, Jaeger-Ruckstuhl CA, Xu Y, Shen BW, Qu A, Polkinghorn C, Friend DJ, Bandaranayake AD, Riddell SR, Kaiser BK, Stoddard BL, Bradley P. Engineering and functionalization of large circular tandem repeat protein nanoparticles. Nature Structural & Molecular Biology. PMID 32203491 DOI: 10.1038/S41594-020-0397-5 |
0.319 |
|
| 2019 |
Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. Elife. 8. PMID 31502535 DOI: 10.7554/Elife.46540 |
0.304 |
|
| 2018 |
Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B. Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Engineering, Design & Selection : Peds. PMID 30566669 DOI: 10.1093/Protein/Gzy031 |
0.359 |
|
| 2018 |
Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Nucleic Acids Research. PMID 30395313 DOI: 10.2210/Pdb6Maf/Pdb |
0.497 |
|
| 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 |
0.341 |
|
| 2018 |
Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Research. PMID 29718463 DOI: 10.1093/Nar/Gky289 |
0.44 |
|
| 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 |
0.372 |
|
| 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 |
0.793 |
|
| 2017 |
Moffett HF, Coon ME, Radtke S, Stephan SB, McKnight L, Lambert A, Stoddard BL, Kiem HP, Stephan MT. Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers. Nature Communications. 8: 389. PMID 28855514 DOI: 10.1038/S41467-017-00505-8 |
0.697 |
|
| 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 |
0.795 |
|
| 2017 |
Rinaldi FC, Doyle LA, Stoddard BL, Bogdanove AJ. The effect of increasing numbers of repeats on TAL effector DNA binding specificity. Nucleic Acids Research. PMID 28460076 DOI: 10.1093/Nar/Gkx342 |
0.453 |
|
| 2017 |
Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Research. 45: 1516-1528. PMID 28180307 DOI: 10.1093/Nar/Gkw1200 |
0.475 |
|
| 2016 |
Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Research. PMID 27913730 DOI: 10.1093/nar/gkw1200 |
0.369 |
|
| 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 |
0.318 |
|
| 2016 |
Stoddard BL, Fox K. Editorial: CRISPR in Nucleic Acids Research. Nucleic Acids Research. 44: 4989-90. PMID 27325109 DOI: 10.1093/Nar/Gkw451 |
0.365 |
|
| 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 |
0.8 |
|
| 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 |
0.815 |
|
| 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 |
0.413 |
|
| 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 |
0.309 |
|
| 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 |
0.335 |
|
| 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 |
0.459 |
|
| 2015 |
Shen BW, Walker B, Lambert A, Stoddard BL, Kaiser BK. The structural basis of asymmetry in DNA recognition and catalysis: binding and cleavage by the I-SmaMI meganuclease Acta Crystallographica Section a Foundations and Advances. 71: s251-s251. DOI: 10.1107/S2053273315096163 |
0.778 |
|
| 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 |
0.303 |
|
| 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 |
0.458 |
|
| 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 |
0.43 |
|
| 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 |
0.46 |
|
| 2014 |
Dynan W, Fox K, Stoddard B. Editorial: NAR surveys the past, present and future of restriction endonucleases. Nucleic Acids Research. 42: 1-2. PMID 24376271 DOI: 10.1093/Nar/Gkt1324 |
0.404 |
|
| 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 |
0.399 |
|
| 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 |
0.365 |
|
| 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 |
0.365 |
|
| 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 |
0.37 |
|
| 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 |
0.422 |
|
| 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 |
0.367 |
|
| 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 |
0.49 |
|
| 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 |
0.751 |
|
| 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 |
0.782 |
|
| 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 |
0.474 |
|
| 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 |
0.488 |
|
| 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 |
0.398 |
|
| 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 |
0.392 |
|
| 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 |
0.469 |
|
| 2012 |
Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D, Stoddard B, Baker D. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Journal of Molecular Biology. 415: 615-25. PMID 22075445 DOI: 10.1016/J.Jmb.2011.10.043 |
0.438 |
|
| 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 |
0.41 |
|
| 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 |
0.516 |
|
| 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 |
0.788 |
|
| 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 |
0.393 |
|
| 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 |
0.511 |
|
| 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 |
0.368 |
|
| 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 |
0.401 |
|
| 2011 |
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, Clair JLS, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. A Biocatalytic Diels-Alder Reaction Using a DesignedEnzyme Synfacts. 2011: 323-323. DOI: 10.1055/S-0030-1259455 |
0.679 |
|
| 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 |
0.799 |
|
| 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 |
0.735 |
|
| 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 |
0.508 |
|
| 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 |
0.441 |
|
| 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 |
0.493 |
|
| 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 |
0.438 |
|
| 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 |
0.49 |
|
| 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 |
0.383 |
|
| 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 |
0.429 |
|
| 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 |
0.504 |
|
| 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 |
0.375 |
|
| 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 |
0.455 |
|
| 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 |
0.396 |
|
| 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 |
0.48 |
|
| 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 |
0.47 |
|
| 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 |
0.798 |
|
| 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 |
0.365 |
|
| 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 |
0.757 |
|
| 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 |
0.623 |
|
| 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 |
0.489 |
|
| 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 |
0.379 |
|
| 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 |
0.436 |
|
| 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 |
0.446 |
|
| 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 |
0.374 |
|
| 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 |
0.489 |
|
| 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 |
0.39 |
|
| 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 |
0.356 |
|
| 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 |
0.505 |
|
| 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 |
0.826 |
|
| 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 |
0.512 |
|
| 2005 |
Stoddard BL. Homing endonuclease structure and function. Quarterly Reviews of Biophysics. 38: 49-95. PMID 16336743 DOI: 10.1017/S0033583505004063 |
0.489 |
|
| 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 |
0.741 |
|
| 2005 |
Scharenberg AM, Rawlings DJ, Monnat RJ, Stoddard BL. 1048. Engineering and Development of I-AniI Homing Endonucleases for Gene Correction Applications Molecular Therapy. 11. DOI: 10.1016/J.Ymthe.2005.07.595 |
0.428 |
|
| 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 |
0.801 |
|
| 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 |
0.608 |
|
| 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 |
0.621 |
|
| 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 |
0.711 |
|
| 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 |
0.502 |
|
| 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 |
0.498 |
|
| 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 |
0.746 |
|
| 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 |
0.353 |
|
| 2004 |
Cotton NJ, Stoddard B, Parson WW. Oxidative inhibition of human soluble catechol-O-methyltransferase. The Journal of Biological Chemistry. 279: 23710-8. PMID 15031283 DOI: 10.1074/Jbc.M401086200 |
0.332 |
|
| 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 |
0.392 |
|
| 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 |
0.692 |
|
| 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 |
0.447 |
|
| 2004 |
Black ME, Mahan SD, Ireton GC, Knoeber C, Stoddard BL. 1030. Engineering Cytosine Deaminase for Suicide Gene Therapy Molecular Therapy. 9. DOI: 10.1016/J.Ymthe.2004.06.975 |
0.305 |
|
| 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 |
0.706 |
|
| 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 |
0.723 |
|
| 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 |
0.419 |
|
| 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 |
0.743 |
|
| 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 |
0.827 |
|
| 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 |
0.403 |
|
| 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 |
0.379 |
|
| 2002 |
Galburt EA, Stoddard BL. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry. 41: 13851-60. PMID 12437341 DOI: 10.1021/Bi020467H |
0.7 |
|
| 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 |
0.823 |
|
| 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 |
0.571 |
|
| 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 |
0.727 |
|
| 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 |
0.76 |
|
| 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 |
0.716 |
|
| 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 DOI: 10.1093/Nar/29.18.3757 |
0.826 |
|
| 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 |
0.595 |
|
| 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 |
0.813 |
|
| 2001 |
Galburt EA, Stoddard BL. Time-resolved macromolecular crystallography Physics Today. 54: 33-39. DOI: 10.1063/1.1397392 |
0.678 |
|
| 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 |
0.429 |
|
| 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 |
0.369 |
|
| 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 DOI: 10.1182/Blood.V96.3.979.015K42A_979_987 |
0.323 |
|
| 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 |
0.823 |
|
| 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 |
0.764 |
|
| 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 |
0.317 |
|
| 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 |
0.789 |
|
| 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 |
0.35 |
|
| 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 DOI: 10.1110/Ps.8.6.1342 |
0.467 |
|
| 1999 |
Stoddard BL. Visualizing enzyme intermediates using fast diffraction and reaction trapping methods: Isocitrate dehydrogenase Biochemical Society Transactions. 27: 42-48. PMID 10093704 DOI: 10.1042/Bst0270042 |
0.309 |
|
| 1999 |
Gottschling DE, Stoddard B. Telomeres: structure of a chromosome's aglet. Current Biology : Cb. 9: R164-7. PMID 10074444 DOI: 10.1016/S0960-9822(99)80103-1 |
0.304 |
|
| 1999 |
Stoddard BL, Jurica M, Heath P, Flick K. The structure, function, and convergent evolution of intron-encoded homing endonucleases Biochemical Society Transactions. 27: A39-A39. DOI: 10.1042/Bst027A039A |
0.318 |
|
| 1999 |
Stoddard BL, Bolduc J, Dyer D, Galburt E, Cohen B, Brubaker M, Mesecar A, Koshland DE, Scott B, Flick K, Jurica M. Time-resolved intermediate trapping and X-ray crystallographic studies of enzyme mechanism: Isocitrate dehydrogenase and nuclease catalysts Biochemical Society Transactions. 27: A2-A2. DOI: 10.1042/Bst027A002B |
0.682 |
|
| 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 DOI: 10.1016/S1097-2765(00)80146-X |
0.494 |
|
| 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 |
0.376 |
|
| 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 |
0.492 |
|
| 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 DOI: 10.1016/S0969-2126(98)00021-5 |
0.442 |
|
| 1998 |
Stoddard BL, Pietrokovski S. Breaking up is hard to do Nature Structural Biology. 5: 3-5. PMID 9437416 DOI: 10.1038/Nsb0198-3 |
0.326 |
|
| 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. DOI: 10.1351/Pac199870010017 |
0.357 |
|
| 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 |
0.306 |
|
| 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 |
0.303 |
|
| 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 |
0.351 |
|
| 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 |
0.487 |
|
| 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 |
0.325 |
|
| 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 |
0.339 |
|
| 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 |
0.311 |
|
| 1996 |
Stoddard BL. Caught in a chemical trap Nature Structural Biology. 3: 907-909. PMID 8901863 DOI: 10.1038/Nsb1196-907 |
0.361 |
|
| 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 |
0.393 |
|
| 1996 |
Brubaker MJ, Dyer DH, Stoddard B, Koshland DE. Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: A catalytic trigger for isocitrate dehydrogenase Biochemistry. 35: 2854-2864. PMID 8608121 DOI: 10.1021/Bi951105V |
0.416 |
|
| 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 DOI: 10.1126/Science.7761851 |
0.425 |
|
| 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 |
0.333 |
|
| 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 |
0.412 |
|
| 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 DOI: 10.1021/Bi00087A009 |
0.389 |
|
| 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 DOI: 10.1021/Bi00087A008 |
0.403 |
|
| 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 DOI: 10.1021/Bi00163A004 |
0.333 |
|
| 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 DOI: 10.1038/358774A0 |
0.359 |
|
| 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 DOI: 10.1073/Pnas.88.13.5503 |
0.385 |
|
| 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 |
0.382 |
|
| 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 DOI: 10.1021/Bi00490A002 |
0.352 |
|
| 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 DOI: 10.1021/Bi00487A008 |
0.35 |
|
| 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 |
0.357 |
|
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