Stoddard Lab Bibliography and Links to Deposited Coordinates (1993 to present)

Intron-encoded homing endonucleases, maturases, REases and gene targeting proteins	Blood coagulation proteins	General enzymology / Time-resolved	Nucleotide synthesis and salvage
	Hydrolases, phosphatases, kinases	Protein Engineering	Reviews and Commentaries

Research Articles (click on top heading of each group to go to research summary page):

(NOTE:  direct links to RCSB pages for crystallographic coordinates are provided at the end of each paper citation)

Intron-encoded homing endonucleases, maturases, restriction endonucleases and gene targeting proteins:

1. 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 endonuclease" Proteins 28: 137 - 139.

2. 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 sequence" Nature Structural Biology 4 (6) 468-476.  Coordinates:  1af5

3. 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 polycephalum" Protein Science 6: 2677 - 2680.  

4. 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-PpoI" Nature 394: 96 - 101. Coordinates:  1a74  1a73  1ipp

5. 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.  Coordinates:  1bp7

6. 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-PpoI" Nature Structural Biology 6: 1096 - 1099. Coordinates:  1cqy  1czo

7. 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 site" J. Mol. Biol. 300(4): 877 - 887.  Coordinates:  1evw  1evx

8. 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 sites" Nature Structural Biology 8 (4): 312 - 316.  Coordinates:  1g9y  1g9z

9. 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) Coordinates:  1mow

10. 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-MsoI" J. Mol. Biol. 329: 253 - 269.  Coordinates:  1m5x 1n3e 1n3f

11. 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.
(See also the corresponding commentary)  Coordinates:    1p8k

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

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

14.  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 positions" J. Mol. Biol. 342 (1): 31 - 41.  Coordinates:    1uoc  1uod

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

16.  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.

17.  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 Nature 441: 656 - 659.  (Also listed under "protein engineering" below)  Coordinates:   2fld 

18.  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 scaffold" Structure 14 (5): 869 - 880.    (Also see this commentary by Fred Gimble)  Coordinates:   2ex5

19.  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 specificities" Nuc. Acids Research 34 (17): 4791 - 800.   Coordinates:  2i3p  2i3q

20.  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.    (Zhao et al. supplementary information)   Coordinates:   2ost

21.  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 endonucleases" Nucleic Acids Research 35 (8): 2748 - 2758.  (Volna et al. supplementary information)

22.  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.   Coordinates:  2o6m

23.  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.   (plus Supplementary Information).  Coordinates:  2qoj

24.  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 endonucleases" Nuc. Acids Res. 35 (21) 7209 - 7221.

25.  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.   (See also this commentary)    (Supplementary Information)  Coordinates:  3bvq   3c25

26.  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 isoschizomers" Nucleic Acids Research 36 (22): 6988 - 6998.  Coordinates:  3e54

27.  Zhao, L., Pellenz, S. and Stoddard, B. L. (2009) "Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I" J. Mol. Biol.  385 (5): 1498 - 1510.
(Supplementary Material)

28.  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. (Supplementary Material)  Coordinates:  3eh8

29.  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.  Coordinates:  3fd2

30.  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 endonuclease" PNAS USA 106 (13): 5099 - 5104.
(Supplementary Material)

31.  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 family" Nucleic Acids Research  37 (8):2560-73.

32.  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 display" Nucleic Acids Research  2009 Sept. 8.  PMID:  19740766.

33. 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 endonuclease" Structure 17: 1368 - 1376.  (Supplementary Material)  Coordinates: 13hi  13hj

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

35.  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 pairs" Nuc. Acids Res. 38 (16) 5601 - 5608.  Coordinates:   3mip   3mis   3ko2

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

37. Mak, A., Lambert, A.R. and Stoddard, B.L. (2010) "Folding, DNA recognition and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI" Structure epub ahead of print PMID: 20800503.  Coordinates:
3mx1    3mx4    3nic

42.  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 target" Science 335: 716 - 719 (PMID 22223736).  Coordinates: 3UGM

   

Hydrolases, Phosphatases and Kinases:

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

2.  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 pyrophosphatase" J. Biol. Chem. 278 (3): 1794 - 1801.  

3.  Shen, B. W., Perraud, A. -L., Scharenberg, A. M and Stoddard, B. L. (2003) "The crystal structure and mutational analysis of human  NUDT9" J. Mol. Biol. 332(2):385-98.  Coordinates:   1qvj     1q33

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

5.  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 channels" J. Biol. Chem. 280 (7): 6138 - 6148.  

   

Blood coagulation factors:

2. 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 structure" Blood 96 (3): 979 - 987.

3. 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 (Plenary Article). Coordinates:  1iqd 

4.  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 VIII" Chemistry and Biology 11 (10): 1413 - 1422.

5.  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 activities" J. Biol. Chem. 279 (51): 53691 - 53698. 

6.  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 VIII" Blood 111 (3): 1240 - 1247.  Coordinates:  1r7e

 

   

General mechanistic enzymology:

2. 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 dehydrogenase" Science 268: 1312 - 1318.   Coordinates:    1ide   1idc

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

4. 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.

5. Brubaker, M., Dyer, D. H., Stoddard, B. L. and Koshland, D. E. Jr. (1995) "Synthesis and characterization of caged isocitrate: a photolytic trigger for enzyme catalysis" (1996) Biochemistry 35: 2854 - 2864.

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

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

8. 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 consequences" Science 277: 202 - 206. Coordinates:  1ai3 1ai2

9. 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.

10. 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 analogues" Nature Structural Biology 5 (10): 891 - 897.  Coordinates:  1bl5

11. 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.  Coordinates:    1a3x 1a3w

12. 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 library" Bioorg. & Med. Chem. Letters 9: 1097 - 1102.

15.  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.
 

   

Nucleoside synthesis and salvage enzymes:

2. 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 coli" Proteins 27: 322 - 324.

3. 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/dehydrogenase" Protein Science 8(6) 1342 - 1349.  Coordinates:  1b0a

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

5. 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. Coordinates:   1k6w 1k70

6. 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. Coordinates:   1ox7 1p6o 

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

8.  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.

9.  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 "protein engineering" below)  Coordinates:  1r9y 1ra5 1r9z 1rak 1r9x 1ra0 

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

11.  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. 

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

   

Protein Engineering:

2.  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.   (See also the corresponding commentary in the same issue) Coordinates:  1qys 

6.  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)  Coordinates:   2fld 

7.  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.  Coordinates: 2erh

8.  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. Coordinates (NMR from Varani Lab):  2GJH

9.  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.  Coordinates: 3b5v     3b5l

10.  Murphy, P., Bolduc, J., Gallaher, J., Stoddard, B. L. and Baker, D. (2009) "Alteration of enzyme specificity by computational loop remodeling and design" PNAS USA 106(23):9215-20. (Also listed under "protein engineering" below).  Coordinates: 3e0l

11. 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 reaction" Science 329: 309 - 313.  Coordinates: 3i1c

12.  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 design" J. Mol. Biol. 15(3): 615 - 625.  Coordinates: 3UD6  3NXF  3O6Y

13.  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 players" Nature Biotech. 30 (2): 190 - 192.  Coordinates: 3UOS

14.  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 hydrolysis" Nature Chem. Biol. Epub ahead of print Feb. 5 PMID 22306579  Coordinates:  3T1G

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2. Stoddard, B. L. (1996) "Laue diffraction: potential for enzyme mechanism and inhibitor screening" Pharmacology and Therapeutics 70 (3): 215 - 256.

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

4. Flick, K. E. and Stoddard, B. L. (1996) "Calcineurin" Current Opinions in Structural Biology 6 (6) 770 - 775.

5. Ellman, J., Stoddard, B. L. and Wells, J. (1997) "Combinatorial Thinking in Chemistry and Biology" PNAS USA 94: 2779 - 2782.

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

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

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

9. 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.

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

11. Gottschling, D. and Stoddard, B. L. (1999) "Telomeres: Structure of a chromosome's aglet" Current Biology 9: R164 - R167. ]

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

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

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

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

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

17.  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. 

18.  Galburt, E. and Stoddard, B. L. (2002) "The catalytic mechanisms of restriction and homing endonucleases" Biochemistry 41 (47): 13851 - 13860.

19.  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.

20.  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) .

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

22.  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.

23.  Chan, S. -H., Stoddard, B. L. and Shuang, X. -U. (2010) "Natural and engineered nicking endonucleases: from cleavage mechanism to engineering of strand-specificity" Nuc. Acids Res. epub ahead of priten (DOI: 10.1093/nar/gkp742).

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

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