Publications

Journal Covers

Galburt, E., Pelletier, J., Wilson G., and Stoddard, B. L. (2002) "Structure of a tRNA repair enzyme and molecular biology workhorse, T4 polynucleotide kinaseStructure 10 (9): 1249 - 1260.

Liu, M., Shen, B. W., Nakaya, S., Pratt, K. P., Fujikawa, K., Davie, E. W., Stoddard, B. L., and Thompson, A. R. (2000) "Hemophilic factor VIII C1 and C2 domain missense mutations and their modeling to the 1.5 angstrom human C2 domain crystal structureBlood 96 (3): 979 - 987.

Heath, P. J., Stephens, K., Monnat, R. and Stoddard, B. L. (1997) "Structure of the I-CreI intron-encoded endonuclease: a novel fold that binds and cleaves a long DNA target sequenceNature Structural Biology 4 (6) 468-476.

Synchotron Radiation News cover

The first Laue data collected at SSRL.  Later used in Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenaseScience 268: 1312 - 1318.

Galburt, E., and Stoddard, B. L. (2001)  "Time-resolved macromolecular crystallography" Physics Today July: pg. 33 - 39.

Spiegel, P. C., Jacquemin, M., St. Remy, J. -M., Stoddard, B. L. and Pratt, K. P. (2001) "Structure of a factor VIII C2 domain/IgG4K Fab complex: identification of an inhibitory antibody epitope on the surface of Factor VIII" Blood 98 (1): 13 - 19.

Eastberg, J., Pelletier, J.., and Stoddard, B. L. (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinaseNuc. Acids Research 32 (2) 653 - 660.

Spiegel, P. C., Murphy, P. and Stoddard, B. L. (2004) "Surface-exposed hemophilic mutations across the Factor VIII C2 domain have variable effects on stability and binding activities" J. Biol. Chem. 279 (51): 53691 - 53698.

Scalley-Kim, M., McConnell-Smith, A., and Stoddard, B. L. (2007) "Coevolution of homing endonuclease specificity and its host target sequence" J. Mol. Biol. 372 (5): 1305 - 1319.

Jurica, M. S. and Stoddard, B. L.  "Homing endonucleases: structure, function and evolutionCellular and Molecular Life Sciences (1999) " 55: 1304 - 1326.

Bolduc, J. M., Spiegel, P. C., Chatterjee, P., Brady, K. L., Downing, M. EW., Caprara, M. G., Waring, R. B. and Stoddard, B. L.(2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor" Genes and Development 17: 2875-2888.

Norimichi, N., Norimichi, Y., Sussman, D., Klein, D. and Stoddard, B. L. (2009) "Recognition of a common rDNA target site by analogous archael LAGLIDADG and eukaryal His-Cys box homing endonucleases isoschizomersNucleic Acids Research 36 (22): 6988 - 6998.


Publications by Project

Intron-Encoded Homing Endonucleases, Maturases, REases and Gene Targeting Proteins  |  Hydrolases, Phospatases, Kinases 
Blood Coagulation Proteins  |  General Enzymology / Time-Resolved  |  Nucleotide Synthesis and Salvage 
Protein Engineering | Reviews and Commentaries

Most recent publications

Dou, J., Vorobieva, A., Sheffler, W., Doyle, L., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Carter, L., Sankaran, B., Ovchinnikov, S., Marcos, E., Huang, P. -S., Vaughan, J. C., Stoddard, B. L. and Baker, D. (2018) “De novo design of a fluorescence-activating beta-barrel” Nature 561: 485 – 491PubMed 30209393   Coordinates: 6D0T  6CZG 6CZH  6CZI  6CZJ

Shen, B.W., Doyle, L., Bradley, P., Heiter, D.F., Lunnen, K.D. Wilson, G. G., and Stoddard, B.L. (2018) "Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI" Nucleic Acids Research  (epub ahead of print).  PMID 3035313Coordinates:  6EG7  6M9G  6MAG   6MAF

Day, A. L., Greisen, P., Doyle, L., Sencha, A., Stella, N., Johnsson, K., Baker, D. and Stoddard, B. (2018) “Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold” Protein Eng Design Selection (epub ahead of print)  PMID 30566669. Coordinates:   5IEN    5IEO   5IEP


Intron-Encoded Homing Endonucleases, Maturases, Restriction Endonucleases and Gene Targeting Proteins

Shen, B.W., Doyle, L., Bradley, P., Heiter, D.F., Lunnen, K.D. Wilson, G. G., and Stoddard, B.L. (2018) "Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI" Nucleic Acids Research  (epub ahead of print).  PMID 3035313Coordinates:  6EG7  6M9G  6MAG   6MAF

Niyonzima, N., Lambert, A. R., Werther, R., De Silva, F. H., Roychoudhury, P., Greninger, AL, Stone, D., Stoddard, B. L. and Jerome, K. R. (2017) "Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analysesProtein Engineering Design and Selection 30 (7):503-522. PMID 28873986   Coordinates:  5V0Q,  5T8D

Moffett, H. F., Coon, M. E., Radteke, S., McKnight, L., Stephan, S. B., McKnight, L., Lambert, A. R., Stoddard, B. L., Kiem, H. -P. and Matthias, S. (2017) "Hit-and-run programming of CAR-T cells using mRNA nanocarriers" Nature Communications 8 (1): 389. doi: 10.1038/s41467-017-00505-8.  PMID 28855514

Werther, R., Hallinan, J. P., Lambert, A., Jarjour, J.,  Havens, K, Galizi, R., Windbichler, N., Crisanti, A., Nolan, T. and Stoddard, B.L. (2017) "Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity" Nuc. Acids Res. 45 (14):8621-8634. PMID 28637173    Coordinates:  5THG   5T2H   5T8D   5T2N   5T2O

Rinaldi, F., Doyle, L. A., Stoddard, B. L.  and Bogdanove, A. (2017) "The effect of increasing numbers of repeats on TAL effector binding specificityNucleic Acids Research 45 (11):6960-6970. PMID 28460076

Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. (2017) "DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target." Nucleic Acids Res. 45 (3):1516-1528.  PMID 27913730  Coordinates:   5TGQ   5TGX     5TH3

Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM and Stoddard BL. (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure 24 (6): 862 - 873.   PMID 27133026   Coordinates:  4YIT    4YIS   4YHX   4Z1X   4LQ0   5ESP   5E5O   4Z20    4Z1Z

Shen, B. W., Walker, B., Lambert, A., Stoddard, B.L., and Kaiser, B.K. (2015) "The structural basis of asymmetry in DNA binding and cleavage as exemplified by the I-SmaMI LAGLIDADG meganucleaseJ. Mol. Biol. 428 (1): 206 - 220.  PMID 26705195   Coordinates:  5E5P   5E5O    4LOX    5ES5     5E63     5E67

Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, Stoddard BL, Windbichler N, Crisanti A. (2014) "A synthetic sex ratio distortion system for the control of the human malaria mosquitoNature Communications 5: 3977.  PMID 24914045

Takeuchi, R., Choi, M., and Stoddard, B.L. (2014) "Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalizationPNAS USA 111 (11): 4061 - 4066.  PMID 24591643

Boissel, S., Jarjour, J., Astrakhan, A., Adey, A., Shendure, J., Stoddard, B. L. Certo, M. T., Baker, D. and Scharenberg, A. (2014) "MegaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering” Nucleic Acids Research 42(4):2591-601.  PMID 24285304

Chan, Y- S., Takeuchi, R., Jarjour, J., Huen, D., Stoddard, B. L. and Russell, S. (2013) “The design and in vivo evaluation of I-OnuI based enzymes for HEG gene drive” PLOS One 8 (9): e74254. PMID 24040217

Metzger, M. J., Stoddard, B. L. and Monmat, R. J. Jr. (2013) “PARP-mediated repair, homologous recombination and backup non-homologous end-joining like repair of single strand nicks” DNA Repair 12 (7): 529 – 534. PMID 23684799

Baxter, S., Lambert, A. R., Kuhar, R., Jarjour, J., Kulshina, N., Parmeggiani, F., Danaher, P., Gano, J., Baker, D., Stoddard, B. L., and Scharenberg, A. M. (2012) "Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleasesNuc. Acids Res. 40 (16): 7985 - 8000. PMID 22684507

Taylor, G. K., Petrucci, L. H., Lambert, A. R., Baxter, S. K., Jarjour, J. and Stoddard, B. L. (2012) "LAHEDES: the LAGLIDADG homing endonuclease database and engineering serverNucleic Acids Research 40 (W1): W110 - W116.  PMID 22570419  Webserver:  http://www.homingendonuclease.net

Kaiser, B. K. and Stoddard, B. L. (2011) "DNA recognition and transcriptional regulation by the WhiA sporulation factorScientific Reports (Nature Press) 1: 156.    PMID 22355671

Jacoby, K., Metzger, M., Shen, B. W., Certo, M. T. Jarjour, J., Stoddard, B. L. and Scharenberg, A. M. (2012) "Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space" Nuc. Acids Res. 40 (11): 4954 - 4964.  PMID 22334611  Coordinates:  3UVF

Mak, A. N., Bradley, P., Cernadas, R. A., Bogdanove, A. J., and Stoddard, B. L. (2012) "The crystal structure of TAL effector PthXo1 bound to its DNA targetScience 335: 716 - 719.  PMID 22223736  Coordinates3UGM

Taylor, G.K., Heiter, D. F., Pietrokovski, S. and Stoddard, B.L. (2011) "Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease familyNuc. Acids Res. 39 (22): 9705 - 9719.  PMID 21890897       Coordinates:  3R3P

Takeuchi, R., Lambert, A. R., Mak, A. N., Jacoby, K., Dickson, R. J., Gloor, G. B., Scharenberg, A. M., Edgell, D. R. and Stoddard, B. L. (2011) "Tapping natural reservoirs of homing endonucleases for targeted gene modificationPNAS USA108(32):13077 - 13082.    PMID 21784983   Coordinates: 3QQY    3R7P

Shen, B. W., Xu, D., Chan, S. H., Zheng, Y., Shu, Z., Xu, S. -Y., and Stoddard, B. L. (2011) "Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSINucleic Acids Research 39 (18):8223-36.  PMID 21724614    Coordinates:  3S1S

Metzger, M. J., McConnell-Smith, A., Stoddard, B. L. and Miller, A. D. (2011) "Single strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV templateNuc. Acids Research  39 (3): 926 - 935. PMID 20876694

Mak, A., Lambert, A.R. and Stoddard, B.L. (2010) "Folding, DNA recognition and function of GIY-YIG endonucleases: crystal structures of R.Eco29kIStructure epub ahead of print PMID 20800503.  Coordinates: 3mx1    3mx4    3nic

Shen, B.W., Heiter, D., Wilson, G. and Stoddard, B.L. (2010) "Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacIStructure 18 (6): 734 - 743. PMID 20541511   Coordinates:  3ldy    3m7k

Ashworth, J., Taylor, G.K., Havranek, J.J., Quadri, S.A. Stoddard, B.L. and Baker, D. (2010) "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairsNuc. Acids Res. 38 (16) 5601 - 5608. PMID 2-435674 Coordinates:   3mip   3mis   3ko2

Thyme, S., Takeuchi, R., Jarjour, J., Scharenberg, A., Stoddard, B. L. and Baker, D. (2009) "Exploitation of homing endonuclease binding energy for catalysis and designNature 461: 1300 - 1304. PMID 19865174

Kaiser, B. K., Clifton, M. C., Shen, B. W. and Stoddard, B. L. (2009) "The structure of a bacterial DUF199 / WhiA protein: domestication of an invasive endonucleaseStructure 1368 - 1376.  PMID 19836336  Coordinates: 13hi  13hj

Jarjour, J., West-Foyle, H., Certo, M. T., Hubert, C. G. Doyle, L., Getz, M. M. Stoddard, B. L. and Scharenberg, A. M. (2009) "High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface displayNucleic Acids Research  2009 Sept. 8.  PMID 19740766.

Dassa, B., London, N., Stoddard, B. L. Schueler-Furman, O. and Pietrokovski, S. (2009) "Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease familyNucleic Acids Research  37 (8):2560-73.  PMID 19264795

McConnell-Smith, A., Takeuchi, R., Pellenz, S., Davis, L., Maizels, N., Monnat, R. J. Jr., and Stoddard, B. L. (2009) "Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonucleasePNAS USA 106 (13): 5099 - 5104.  PMID 19276110

Li, H., Pellenz, S., Ulge, U., Stoddard, B. L. and Monnat, R. J. Jr. (2009) "Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins" Nucleic Acids Research 37 (5): 1650 - 1662.  PMID 19153140  Coordinates:  3fd2

Takeuchi R, Certo M, Caprara MG, Scharenberg AM, and Stoddard BL. (2009) "Optimization of the in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation" 37 (3): 877 - 890.  PMID 19103658 Coordinates:  3eh8

Zhao, L., Pellenz, S. and Stoddard, B. L. (2009) "Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803IJ. Mol. Biol.  385 (5): 1498 - 1510. PMID 19038269

Nomura, N., Nomura, Y., Sussman, D., Klein, D. and Stoddard, B. L. (2008) "Recognition of a common rDNA target site by analogous archael LAGLIDADG and eukaryal His-Cys box homing endonucleases isoschizomersNucleic Acids Research 36(22): 6988 - 6998. PMID 18400177  Coordinates:  3e54

Lambert, A. R., Sussman, D., Shen, B. W., Nix, J., Maunus, R., Samuelson, J., Xu, S. -Y., and Stoddard, B. L. (2008) "Structures of the rare cutting restriction endonuclease NotI revieal a novel metal binding fold involved in DNA recognition" Structure 16: 558 - 569.   PMID 18400177    Coordinates:  3bvq   3c25

Eastberg, J. H., McConnell-Smith, A., Zhao, L., Ashworth, J., Shen, B. W. and Stoddard, B. L. (2007) "The thermodynamics of DNA target site recognition by homing endonucleasesNuc. Acids Res. 35 (21) 7209 - 7221. PMID 17947319

Scalley-Kim, M., McConnell-Smith, A. and Stoddard, B. L. (2007) "Coevolution of homing endonuclease specificity and its host target sequenceJ. Mol. Biol. 372 (5): 1305 - 1319.  PMID 17720189  Coordinates:  2qoj

Eastberg, J., Monnat, R. J. Jr., and Stoddard, B. L. (2007) “Mutability of the ββα-metal HNH nuclease active site: substitution of a deprotonation mechanism” Biochemistry 46 (24): 7215 - 7225. PMID 17416660  Coordinates:  2o6m

Volna, P., Jarjour, J., Baxter,S., Roffler, S. R., Monnat, R. J. Jr., Stoddard, B. L. and Scharenberg, A. M(2007) "Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleasesNucleic Acids Res. 35 (8): 2748 - 2758.  PMID 17426121

Zhao, L, Boncora, R., Shub, D. and Stoddard, B. L. (2007) “The restriction folds turns to the dark side: a bacterial homing endonuclease with a PD(D/E)XK motif”  EMBO Journal 26: 2432 - 2442. PMID 17410205   Coordinates:   2ost

Rosen, L. E., Morrison, H. A., Masri, S., Brown, M. J., Springstubb, B., Sussman, D., Stoddard, B. L. and Seligman, L. M. (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificitiesNuc. Acids Res. 34 (17): 4791 - 800. PMID 16971456   Coordinates:  2i3p  2i3q

Spiegel, P. C., Chevalier, B., Sussman, D., Turmel, M., Lemieux, and Stoddard, B. L. (2006) "The structure of I-CeuI homing endonuclease: evolving asymmetric DNA recognition from a symmetric protein scaffoldStructure 14 (5): 869 - 880. PMID 16698548  Coordinates: 2ex5

Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J. Jr., Stoddard, B. L. and Baker, D. (2006) "Computational redesign of endonuclease DNA binding and cleavage specificityNature  441: 656 - 659.  (Also listed under "protein engineering" below) PMID 16738662  Coordinates:   2fld

Landthaler, M., Shen, B.W., Stoddard, B. L. and Shub, D.A.  (2006) "Two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities" J. Mol. Biol. 358 (4): 1137 - 1151. PMID 16569414

Chevalier, B., Sussman, D., Otis, C., Noel, A. -J., Turmel, M., Lemieux, C., Stephens, K., Monnat, R. J. Jr. and Stoddard, B. L.  (2004) "Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease " Biochemistry  43: 14015 - 14026. PMID 15518550  Coordinates: 1t9j 1t9i

Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R. J. Jr., Stoddard, B. L. and Seligman, L. (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positionsJ. Mol. Biol. 342 (1): 31 - 41. PMID 15313605  Coordinates: 1uoc  1uod

Shen, B. W., Landthaler, M., Shub, D. A. and Stoddard, B. L.  (2004) "DNA binding and cleavage by the HNH homing endonuclease I-HmuIJ. Mol. Biol. 342 (1): 34 - 56.  PMID 15313606 Coordinates:  1u3e

Bakhrat, A., Jurica, M. S., Stoddard, B. L. and Raveh, D. (2004) "Homology modeling and mutational analysis of HO endonuclease of yeastGenetics 166: 721 - 728. PMID 15020462

Bolduc, J. M., Spiegel, P. C., Chatterjee, P., Brady, K. L., Downing, M. EW., Caprara, M. G., Waring, R. B. and Stoddard, B. L. (2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor" Genes and Development 17: 2875-2888. PMID 1463397  Coordinates: 1p8k

Chevalier, B., Turmel, M., Lemieux, C., Monnat, R. J. Jr. and Stoddard, B. L. (2003) "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoIJ. Mol. Biol. 329: 253 - 269. PMID 12758074  Coordinates: 1m5x 1n3e 1n3f

Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) "Design, activity and structure of a highly specific artificial endonuclease" Molecular Cell 10 :895 - 905. (Also listed under "protein engineering" below) PMID 12419232 Coordinates:  1mow

Chevalier, B., Monnat, R. J. Jr. and Stoddard, B. L. (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between two active sitesNature Structural Biology 8 (4): 312 - 316. PMID 11276249  Coordinates:  1g9y  1g9z

Galburt, E., Jurica, M., Chevalier, B., Erho, D., Tang, W., Monnat, R. J. Jr., and Stoddard, B. L. (2000) "Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active siteJ. Mol. Biol. 300(4): 877 - 887. PMID 10891275  Coordinates:  1evw  1evx

Galburt, E., Chevalier, B., Tang, W., Jurica, M. S., Flick, K. E., Monnat, R. J. Jr., and Stoddard, B. L. (1999) "A novel endonuclease mechanism directly visualized for I-PpoINature Structural Biology 6: 1096 - 1099. PMID 10581547  Coordinates: 1cqy  1czo

Jurica, M. S., Monnat, R. J. Jr. and Stoddard, B. L. (1998) "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI" Molecular Cell 2: 469 - 476. PMID 9665136  Coordinates:  1bp7

Flick, K.E., Jurica, M. S., Monnat, R. J. Jr., and Stoddard, B. L. (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoINature 394: 96 - 101. PMID 9665136 Coordinates:  1a74  1a73  1ipp

Flick, K.E., McHugh, D., Heath, J.D., Stephens, K.M., Monnat, R.J. Jr., and Stoddard, B.L. (1997) "Crystallization and preliminary X-ray studies of I-PpoI: a nuclear, intron-encoded homing endonuclease from Physarum polycephalumProtein Science 6: 2677 - 2680.   PMID 9416623

Heath, P. J., Stephens, K., Monnat, R. and Stoddard, B. L. (1997) "Structure of the I-CreI intron-encoded endonuclease: a novel fold that binds and cleaves a long DNA target sequenceNature Structural Biology 4 (6) 468-476. PMID 9187655  Coordinates:  1af5

Stephens, K., Monnat, R. Heath, P.J. and Stoddard, B. L. (1997) "Crystallization and preliminary x-ray characterization of I-CreI: an intron-encoded restriction endonucleaseProteins 28: 137 - 139. PMID 9144800


Hydrolases, Phosphatases and Kinases

Perraud., A. -L., Takanishi, C., Shen, B. W., Kang, S., Smith, M. K., Schmitz, C., Knowles, H. M., Ferraris, D., Li, Weixing, Zhang, J., Stoddard, B. L. and Scharenberg, A. M. (2005) "Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channelsJ. Biol. Chem. 280 (7): 6138 - 6148. PMID 15561722

Eastberg, J., Pelletier, J., and Stoddard, B. L. (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinaseNucleic Acids Research 32 (2): 653 - 660.  PMID 14754987 Coordinates:  1rc8   1rpz    1rrc

Shen, B. W., Perraud, A. -L., Scharenberg, A. M and Stoddard, B. L. (2003) "The crystal structure and mutational analysis of human  NUDT9J. Mol. Biol. 332(2):385-98. PMID 12948489  Coordinates:   1qvj     1q33

Perraud, A. -L., Shen, B., Dunn, C. A., Rippe, K., Smith, M. K., Bessman, M. J., Stoddard, B. L. and Scharenberg, A. M. (2003) "NUDT9, a member of the nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphataseJ. Biol. Chem. 278 (3): 1794 - 1801. PMID 12427752

Galburt, E., Pelletier, J., Wilson G., and Stoddard, B. L. (2002) "Structure of a tRNA repair enzyme and molecular biology workhorse, T4 polynucleotide kinaseStructure 10 (9): 1249 - 1260. PMID 12220496  Coordinates:  1ltq


Blood Coagulation Factors

Shen, B. W., Spiegel, P.C., Chang, C. -H., Huh, J. -W., Lee, J. -S., Kim, J., Kim, Y. -H. and Stoddard, B. L. (2008) "Tertiary structure and domain organization of coagulation factor VIIIBlood 111 (3): 1240 - 1247.  PMID 17965321 Coordinates:  1r7e

Spiegel, P. C. and Stoddard, B. L. (2004)  "Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activitiesJ. Biol. Chem. 279 (51): 53691 - 53698. PMID 15471879

Spiegel, P.C., Kaiser, S. M., Simon, J. and Stoddard, B. L. (2004) "Disruption of protein-membrane binding and identification of small molecule inhibitors of coagulation factor VIIIChemistry and Biology 11 (10): 1413 - 1422. PMID 15489168

Spiegel, P. C., Jacquemin, M., St. Remy, J. -M., Stoddard, B. L. and Pratt, K. P. (2001) "Structure of a factor VIII C2 domain/IgG4K Fab complex: identification of an inhibitory antibody epitope on the surface of Factor VIII" Blood 98(1): 13 - 19. PMID 11418455  Coordinates:  1iqd

Liu, M., Shen, B. W., Nakaya, S., Pratt, K. P., Fujikawa, K., Davie, E. W., Stoddard, B. L., and Thompson, A. R. (2000) "Hemophilic factor VIII C1 and C2 domain missense mutations and their modeling to the 1.5 angstrom human C2 domain crystal structureBlood 96 (3): 979 - 987. PMID 10910913

Pratt, K. P., Shen, B. W., Takeshima, K., Davie, E. W., Fujikawa, K. and Stoddard, B. L. (1999) "Structure of the C2 domain of human factor VIII at 1.5 angstrom resolutionNature 402: 439 - 442.  PMID 10586887  Coordinates:  1d7p


General Mechanistic Enzymology

Cotton, N. J., Stoddard, B. L. and Parson, W. W. (2004) "Oxidative inhibition of soluble human catechol-o-methyltransferase" J. Biol. Chem. 279: 23710 - 23718.  PMID 15031283

Bond, C., Jurica, M. S., Mesecar, A. and Stoddard, B. L. (2000) "Determinants of allosteric activation of yeast pyruvate kinase and identification of novel effectors using computational screeningBiochemistry 39: 15333  - 15343.  PMID 11112519

Bond, C. J., Huang, J. -Y., Hajduk, R., Heath, P. J., Flick, K. E., and Stoddard, B. L(2000) "Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis" Acta Cryst D56 1359 - 1366.   PMID 11053832  Coordinates:  1dt0

Bryant, M. D., Flick, K. E., Koduri, R. S., Wilton, D. C., Stoddard, B. L., and Gelb, M. H. (1999) "1,3-dioxane-4,6-dione-5-carboxamide-based inhibitors of human group IIA phospholipase A2: X-ray structure of the complex and interfacial selection of inhibitors from a structural libraryBioorg. & Med. Chem. Letters  9: 1097 - 1102.  PMID 10328292

Jurica, M. S., Heath, P. J., Shi, W., Mesecar, A., and Stoddard, B. L. (1998) "The allosteric regulation of pyruvate kinase by fructose-1,6-bis-phosphate" Structure 6 (2) 195 - 210.  PMID 2202599   Coordinates:    1a3x 1a3w

Stoddard, B. L., Cohen, B., Brubaker, M., Mesecar, A. and Koshland, D. E. Jr. (1998) "Millisecond Laue structures of an enzyme product complex using photocaged substrate analoguesNature Structural Biology 5 (10): 891 - 897.  PMID   9783749   Coordinates:  1bl5

Cohen, B. E., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Caged NADP and NAD. "Synthesis and characterization of functionally distinct caged compounds." Biochemistry 36: 9035 - 9044.  PMID 9220992

Mesecar, A., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequencesScience 277: 202 - 206.  PMID 9211842  Coordinates:  1ai3 1ai2

Scott, W. G., Stoddard, B. L. and Klug, A. (1996) "Capturing structures of catalytic RNA intermediates: the hammerhead ribozymeScience 274: 2065 - 2069.   PMID 8953035

Stoddard, B. L., Dean, A. and Bash, P. A. (1996) "Combining Laue diffraction and molecular dynamics to study enzyme intermediates: formation of a Michaelis complexNature Struct. Biol. 3 (7): 590 - 594. PMID 8673502

Brubaker, M., Dyer, D. H., Stoddard, B. L. and Koshland, D. E. Jr. (1995) "Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: a catalytic trigger for isocitrate dehydrogenase" (1996) Biochemistry 35: 2854 - 2864. PMID 8608121

O'Hara, P., Goodwin, P. and Stoddard, B. L. (1995) "Determination of substrate diffusion rates in protein crystals by optical microspectrophotometry using CCD video analysis" J. Appl. Cryst. 28: 829 - 833.  

Stoddard, B. L. and Farber, G. K. (1995) "Direct measurement of steady-state kinetic constants in the enzyme crystalStructure 3: 991 - 996.  PMID 8590009

Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenaseScience 268: 1312 - 1318.   PMID 7761851  Coordinates:    1ide   1idc

Lee, M., Klein, O. D., Bolduc, J., Dyer, D. H., Stoddard, B. L. and Koshland, D. E. Jr. (1995) "The role of the catalytic residues Lysine 230 and Tyrosine 160 in the NADP+-dependent isocitrate dehyrogenaseBiochemistry 34: 378 - 384. PMID 7819221


Nucleoside Synthesis and Salvage Enzymes

Fuchita, M., Ardiani, A., Zhao, L., Serve, K., Stoddard, B. L. and Black, M.E. (2009) "Bacterial Cytosine Deaminase Mutants Created by Molecular Engineering Show Improved 5FC-Mediated Cell Killing In Vitro and In VivoCancer Research 69 (11): 4791-9.  PMID 19487291   Coordinates: 3g77

Murphy, P., Bolduc, J., Gallaher, J., Stoddard, B. L. and Baker, D. (2009) "Alteration of enzyme specificity by computational loop remodeling and designPNAS USA 106 (23): 9215-20. (Also listed under "protein engineering" below).   PMID 18291415  Coordinates: 3eol

Stolworthy, T.S., Korkegian, A. M., Willmon, C. L., Ardiani, A., Cundiff, J., Stoddard, B. L. and Black, M.E.  (2008) "Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine" J. Mol. Biol 377 (3): 854 - 869. 

Korkegian, A., Baker, D. and Stoddard, B. L. (2005) "Computational thermostabilization of an enzyme" Science 308: 857 - 860 (Also listed under "protein engineering" below).  PMID 15879217    Coordinates: 2o3k  1ysb  1ysd

Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) “Random mutagenesis and selection of Escherichia colo cytosine deaminase for cancer gene therapy”  Protein Engineering and Design 17 (8): 225 – 633. (Also listed under "protein engineering" below).  PMID 15381761     Coordinates:  1r9y 1ra5 1r9z 1rak 1r9x 1ra0

Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) "Alanine-Scanning Mutagenesis Reveals a Cytosine Deaminase Mutant with Altered Substrate Preference" Biochemistry 43: 8957 - 8964.  PMID 15248753

Ireton, G. and Stoddard, B. L. (2004) "Microseed matrix screening to improve crystals of yeast cytosine deaminase" Acta Cryst D 60: 601 - 605.  PMID 14993707   Coordinates:  1rb7

Ireton, G., Black, M. and Stoddard, B. L. (2003) "The 1.14 Å crystal structure of yeast cytosine deaminase:  evolution of nucleotide salvage enzymes and implications for genetic chemotherapy" Structure 11(8): 961 - 972.   PMID  12905827  Coordinates:   1ox7 1p6o

Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2002) "The structure of Escherichia coli cytosine deaminase" J. Mol. Biol. 315(4): 687 - 697.  PMID 11812140  Coordinates:   1k6w 1k70

Ireton, G., Black, M., and Stoddard, B. L. (2001) "Crystallization and prelminary X-ray analysis of bacterial cytosine deaminaseActa Cryst D 57: 1643 - 1645.   PMID 11679731

Shen, B. W., Dyer, D. H., Huang, J. -Y., D'Ari, L., Rabinowitz, J., and Stoddard, B. L. (1998) "The crystal structure of a bacterial bifunctional 5,10-methylene tetrahydrofolate cyclohydrolase/dehydrogenaseProtein Science 8(6) 1342 - 1349.   PMID 10386884   Coordinates:  1b0a

Cheung, E., D'Ari, L., Rabinowitz, J. C., Dyer, D. H. and Stoddard, B. L. (1997) "Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coliProteins 27: 322 - 324.  PMID 9061797

D'Ari, L., Cheung, E., Rabinowitz, J., Bolduc, J. and Stoddard, B. L. (1997) "Purification, crystallization, and preliminary x-ray Data for 10-formyl-tetrahydrofolate synthetase from Clostridium acidi-uriciProteins 27: 319 - 321.  PMID 9061796


Protein Engineering

(Please note that some of these papers are also listed under their respective biological functions, above.)

Day, A. L., Greisen, P., Doyle, L., Sencha, A., Stella, N., Johnsson, K., Baker, D. and Stoddard, B. (2018) “Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold” Protein Eng Design Selection (epub ahead of print December 2018)  PMID 30566669. Coordinates:   5IEN    5IEO   5IEP

Dou, J., Vorobieva, A., Sheffler, W., Doyle, L., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Carter, L., Sankaran, B., Ovchinnikov, S., Marcos, E., Huang, P. -S., Vaughan, J. C., Stoddard, B. L. and Baker, D. “De novo design of a fluorescence-activating beta-barrel” Nature 561: 485 – 491PubMed 30209393   Coordinates: 6D0T  6CZG 6CZH  6CZI  6CZJ

Dou, J., Doyle, L., Greisen, P., Schena, A., Park, H., Johnsson, K., Stoddard, B.L., and Baker, D. (2017) "Sampling and energy evaluation challenges in ligand binding protein designProtein Science Oct 4.  doi 10.1002/pro.3317.  PMID 28980354   Coordinates: 5IER   5IF6

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, Fairlie WD, Hockenbery DM, Baker D. (2016) "Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancereLife Nov 2;5. pii: e20352. doi: 10.7554/eLife.20352.  PMID 27805565  Coordinates: 5JSB    5JSN

King, I.C., Gleixner, J., Doyle, L., Kusin, A., Hunt, J. F., Xiao, R., Montelione, G. T., Stoddard, B. L. , Dimaio, F. and Baker, D. (2015) "Precise assembly of complex beta sheet topologies from de novo designed building blockseLife doi: 10.7554/eLife.11012. [Epub ahead of print]PMID 26650357  Coordinates: 5CW9

Doyle, L. A., Hallinan, J. P., Bolduc, J. M., Stoddard, B. L. and Bradley, P. (2015) "Rational design of alpha-helical tandem repeat proteins with closed architecturesNature 528: 585 - 588. PMID 26675735  Coordinates: 4YXX   4YXY  4YXZ 4YY2  4YY5  5BYO

Siegel, J. B., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E., and Baker, D. (2015) "Computational enzyme design enables a novel one-carbon assimiliation pathwayPNAS USA 112 (12): 3704-3709. PMID 25775555 Coordinates:  4QPZ  4QQ8

Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. (2015) "Control of repeat-protein curvature by computational protein designNature Struct. Mol. Biol. Jan 12. doi: 10.1038/nsmb.2938. [Epub ahead of print] PMID 25580576  Coordinates:  4R6G   4R5C   4R58   4R5D  4R6F

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, and Baker D. (2014) "A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cellsCell 157 (7): 1644 - 1656.  PMID 24949974  Coordinates:  4OYD

Mills, J., Khare, S., Bolduc, J., Forouhar, F., Lew, S., Seetharaman, J., Tong, L., Stoddard, B. L. and Baker, D. (2013) “Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy” J. Am. Chem. Soc. 135(36):13393 – 13399.  PMID 23924187)   Coordinates:   4IXO    4IWW

Tinberg, C., Khare, S.D., Dou, J., Doyle, L., Nelson, J., Schena, A., Johnsson, K., Stoddard, B. L. and Baker, D. “Computational Design of Ligand Binding Proteins with High Affinity and Selectivity” (2013) Nature  501: 212 – 216.  (PMID  24005320)   Coordinates:   4J8T   4J9A

Khare, S.D., Kipnis, Y., Greisen, P.J., Takeuchi, R., Ashani, Y., Goldsmith, M., Song, Y., Gallaher, J.L., Silman, Il., Leader, H., Sussman, J.L., Stoddard, B.L., Tawfik, D.S., and Baker, D. (2012) "Computational redesign of a mononuclease zinc metalloenzyme for organophosphate hydrolysisNature Chem. Biol. 8 (3):294-300 PMID 22306579  Coordinates:  3T1G

Eiben, C.B., Siegel, J.B., Bale, J.B., Cooper, S., Khatib, F., Shen, B.W., Payers, F., Stoddard, B.L. Popovic, Z., and Baker, D. (2012) "Increased Diels-Alderase activity through backbone remodeling guided by FoldIt playersNature Biotech. 30(2): 190 - 192. PMID 22267011  Coordinates3UOS

Wang, L., Althoff, E. A., Bolduc, J., Moody, J., Lassila, J. K., Giger, L., Hilvert, D., Stoddard, B.L. and Baker, D. (2012) "Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme designJ. Mol. Biol. 15 (3): 615 - 625. PMID 22075445  Coordinates3UD6  3NXF  3O6Y

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.  (2010) "Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reactionScience 329: 309 - 313. PMID 20647463 Coordinates3i1c

Murphy, P., Bolduc, J., Gallaher, J., Stoddard, B. L. and Baker, D. (2009) "Alteration of enzyme specificity by computational loop remodeling and designPNAS USA 106 (23):9215-20. (Also listed under "nucleotide salvage and synthesis enzymes" above).  PMID 18291415   Coordinates3e0l

Jiang, L, Althoff, E. A., Clemente, F. R., Doyle, L., Rothlisberger, D., Zanghellini, A., Gallaher, J. L., Betker, J. L., Tanaka, F., Barbas, C. F., Hilvert, D., Houk, K. N., Stoddard, B. L. and Baker, D. (2008) "De Novo computational design of retro-aldol enzymes" Science 319 : 1387 - 1391.  PMID 18323453   Coordinates: 3b5v    3b5l

Dantas, G., Watters, A.L., Lunde, B. M., Eletr, Z. M., Isern, N.G., Roseman, T., Lipfert, J., Doniach, S., Tompa, M., Kuhlman, B., Stoddard, B. L., Varani, G. and Baker, D. (2006) "Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution" J. Mol. Biol. 362 (5): 1004 - 1024.   PMID 16949611  Coordinates (NMR from Varani Lab):  2GJH

Joachimiak, L.A., Kortemme, T., Stoddard, B. L., and Baker, D. (2006) "Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface" J. Mol. Biol. 361 (1): 195-208.  PMID 16831445  Coordinates2erh

Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J. Jr., Stoddard, B. L. and Baker, D. (2006) "Computational redesign of endonuclease DNA binding and cleavage specificity" Nature 441: 656 - 659. (Also listed under "intron-encoded proteins" above)   PMID 16738662 Coordinates:   2fld

Korkegian, A., Baker, D. and Stoddard, B. L. (2005) "Computational thermostabilization of an enzyme catalyst" Science 308: 857 - 860 (Also listed under "nucleotide synthesis and salvage enzymes" above).  PMID 15879217  Coordinates: 2o3k  1ysb  1ysd

Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) “Directed evolution and selection of bacterial cytosine deaminase with altered substrate specificity towards 5-fluorocytosine”  Protein Engineering and Design 17 (8): 225 – 633. (Also listed under "nucleotide synthesis and salvage enzymes" above).  PMID 15381761   Coordinates:  1r9y 1ra5 1r9z 1rak 1r9x 1ra0

Kortemme, T., Joachimiak, L. A., Bullock, A. N., Stoddard, B. L. and Baker, D. (2004) "Computational redesign of protein-protein interaction specificity" Nature Structural and Molecular Biology 11: 371 - 379.  PMID 15034550    Coordinates:   1ujz

Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. and Baker, D. (2003) "Design of a novel globular protein fold with atomic accuracy" Science 302: 1364 - 1368.  PMID 14631033   Coordinates:  1qys

Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) "Design, activity and structure of a highly specific artificial endonuclease" Molecular Cell 10 : 895 - 905 (Also listed under "intron-encoded proteins" above).   PMID 12419232   Coordinates:  1mow


Reviews and Commentaries

Bogdanove, A.J., Bohm, A., Miller, J.C., Morgan, R.D. and Stoddard, B.L. (2018) "Engineering altered protein-DNA recognition specificityNucleic Acids Res. (Epub ahead of print) doi: 10.1093/nar/gky289.  PMID 29718463

Stoddard, B.L., Khvorova, A., Corey, D.R., Dynan, W.S. and Fox, K.R. (2018) "Editorial: Nucleic Acids Research and Nucleic Acid TherapeuticsNucleic Acids Res. 46 (4): 1563 - 1564.  PMID 29506274

Stoddard, B.L. and Fox, K.R. (2016) "Editorial: CRISPR in Nucleic Acids ResearchNucleic Acids Res. 44 (17): 8512.  PMID 27382068

Jeltsch, A., Wende, W., Friedhoff, P., and Stoddard, B. L. (2015) "Alfred Pingoud (1945 - 2015)Nucleic Acids Res. 43(16): 7661 - 7663. PMID 26385498

Corey DR, Wise JA, Fox KR, Stoddard BL. (2015) "Breakthrough articles: putting science firstNucleic Acids Research 42(18):11273-4.  PMID 25301802

Takeuchi R, Choi M, and Stoddard BL. (2015) "Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimizationMethods in Molecular Biology 1239: 105-32.   PMID 25408403

Stoddard, B. L. (2014) "Homing endonucleases from mobile group I introns: discovery to genome engineeringMobile DNA 5(1): 7   PMID 24589358

Zhao, L. and Stoddard, B. L. (2014) "Rapid determination of homing endonuclease DNA binding specificity profiles" in Methods in Enzymology 1123: 127 - 13.4   PMID 24510265

28.  Doyle, E. L, Stoddard, B. L., Voytas, D. F., and Bodganove, A. J. (2013) "TAL effectors: high adaptable phytobcterial virulence factors and readily engineered DNA-targeting proteins.”  Trends Cell Biol. 23 (8): 390-8 PMID 23707478

Mak, A. N. -S., Bradley, P., Bogdanove, P. and Stoddard, B. L. (2013) "TAL effectors: structure, mechanism, engineering and applicationsCurrent Opinions in Structural Biology 23 (1): 93 - 99.   PMID 23265998

Taylor, G. K. and Stoddard, B. L. (2012) "Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organismsNuc. Acids Res. 40 (12): 5189 - 5200.   PMID 22406833

Stoddard, B.L. (2011) "Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modificationStructure 19 (1): 7 - 15.  PMID 21220111

Stoddard, B.L. and Belfort, M. (2010) "Social networking by mobile introns and their host genesMolecular Microbiology 78(1): 1 - 4.  PMID 20545861

Chan, S. -H., Stoddard, B. L. and Shuang, X. -U. (2010) "Natural and engineered nicking endonucleases: from cleavage mechanism to engineering of strand-specificityNuc. Acids Res. 39 (1): 1 - 18.  PMID 20805246

Monnat, R. J. Jr., Scharenberg, A. M. and Stoddard, B. L. (2008) "Progress in engineering homing endonucleases for gene targeting: ten years after structures "  Progress in Gene Therapy Volume 3: Autologous and cancer stem cell gene therapy (R. Bertolotti and K. Ozawa, ed.) World Scientific Publishers.   

Stoddard, B. L. (2005) "Homing endonuclease structure and function" Quarterly Reviews in Biophysics 38 (1): 49 - 95.  PMID 16335743

Chevalier, B., Monnat, R. J. Jr. and Stoddard, B. L. (2005) "The LAGLIDADG homing endonuclease family" in Homing endonucleases and Inteins (Springer Verlag; M. Belfort, V. Derbyshire, D. Wood and B. Stoddard, editors) .

Roberts, R., et al., Stoddard, B. L. et al. (2003) "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes" Nucl. Acids. Res. 31 (7): 1805 - 1812.   PMID 12654995

Galburt, E. and Stoddard, B. L. (2002) "Catalytic mechanisms of restriction and homing endonucleasesBiochemistry 41(47): 13851 - 13860.   PMID 12437341

Spiegel, P. C. and Stoddard, B. L. (2002) "Optimization of factor VIII replacement therapy: can structural studies help evade antibody inhibitors?British Journal of Haematology 119: 310 - 322.  PMID 12406063

Chevalier, B. and Stoddard, B. L. (2001) "Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobilityNucleic Acids Research 28(18): 3757-3774.  PMID 11557808

Galburt, E., and Stoddard, B. L. (2001) "Time-resolved macromolecular crystallography" Physics Today July: pg. 33 - 39.

Stoddard, B. L. (2001) "Accumulation and trapping of catalytic intermediates for crystallographic structure determination" Methods 24: 125 - 138.

Galburt, E. and Stoddard, B. L. (2000) "Restriction endonucleases: one of these things is not like the othersNature Structural Biology 7(2): 89 - 91.  PMID 10655603

Ren, Z., Bourgeois, D., Helliwell, J. R., Moffat, K., Srajer, V. and Stoddard, B. L. (1999) "Laue Crystallography: Coming of AgeJournal of Synchrotron Radiation 6: 891 - 917. 

Gottschling, D. and Stoddard, B. L. (1999) "Telomeres: Structure of a chromosome's agletCurrent Biology 9: R164 - R167.   PMID 10074444

Jurica, M. S. and Stoddard, B. L. (1999) "Homing endonucleases: structure, function and evolutionCellular and Molecular Life Sciences 55: 1304 - 1326.   PMID 10487208

Stoddard, B. L., Bolduc, J. M., Dyer, D. H., Scott, W. G. and Sweet, R.M. (1998) "Visualizing enzyme and ribozyme intermediates using fast diffraction and reaction trapping methods" Pure and Applied Chemistry 70 (1): 17 - 23.

Stoddard, B. L. (1998) "New results from time-resolved crystallographyCurr. Opin. Struct. Biol. 8: 612 - 618.  PMID 9818266

Jurica, M. S. and Stoddard, B. L. (1998) "Mind your Bs and Rs: Bacterial Chemotaxis, signal transduction, and protein recognitionStructure 6: 809 - 813.  PMID 9687374

Stoddard, B. L. and Pietrokovski, S. (1998) "Breaking up is hard to doNature Structural Biology 5 (1): 3 - 6.  PMID 9437416

Ellman, J., Stoddard, B. L. and Wells, J. (1997) "Combinatorial Thinking in Chemistry and BiologyPNAS USA 94: 2779 - 2782.   PMID 9096292

Flick, K. E. and Stoddard, B. L. (1996) "CalcineurinCurrent Opinions in Structural Biology 6 (6) 770 - 775.  PMID 8994877

Stoddard, B. L. (1996) "Caught in a chemical trapNature Structural Biology 3 (11): 907 - 909.   PMID 8901863

Stoddard, B. L. (1996) "Intermediate Trapping and Laue X-ray diffraction: potential for enzyme mechanism, dynamics and inhibitor screeningPharmacology and Therapeutics 70 (3): 215 - 256.  PMID 8888067

Stoddard, B. L., Farber, G. K., and Strong, R. K. (1993) "Facts and Fancy of Microgravity Protein CrystallizationBiotechnology and Genetic Engineering Reviews 11: 57 - 77.   PMID 7840348