B. Stoddard

发表

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Z. Popovic, D. Baker, Firas Khatib, 2012, Nature Biotechnology.

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

D. Baker, B. Stoddard, B. Kuhlman, 2003, Science.

Computational Thermostabilization of an Enzyme

B. Stoddard, A. Korkegian, M. Black, 2005, Science.

De Novo Computational Design of Retro-Aldol Enzymes

Eric A. Althoff, Jasmine L. Gallaher, D. Baker, 2008, Science.

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

Jasmine L. Gallaher, D. Baker, J. Siegel, 2010, Science.

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface.

D. Baker, B. Stoddard, T. Kortemme, 2006, Journal of molecular biology.

Prediction of the structure of a receptor–protein complex using a binary docking method

D. Koshland, B. Stoddard, 1992, Nature.

A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.

J. Heitman, J. V. Van Etten, B. Stoddard, 2003, Nucleic acids research.

Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme

B. Stoddard, A. Klug, W. Scott, 1996, Science.

Computational redesign of protein-protein interaction specificity

D. Baker, B. Stoddard, T. Kortemme, 2004, Nature Structural &Molecular Biology.

Computational protein design enables a novel one-carbon assimilation pathway

Amanda L. Smith, Jasmine L. Gallaher, D. Baker, 2015, Proceedings of the National Academy of Sciences.

Design, activity, and structure of a highly specific artificial endonuclease.

B. Stoddard, T. Kortemme, R. Monnat, 2002, Molecular cell.

The structure of I-Crel, a Group I intron-encoded homing endonuclease

B. Stoddard, R. Monnat, P. Heath, 1997, Nature Structural Biology.

Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine.

B. Stoddard, A. Korkegian, M. Black, 2008, Journal of molecular biology.

Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.

D E Koshland, R M Sweet, D. Koshland, 1995, Science.

Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli.

D E Koshland, D. Koshland, B. Stoddard, 1995, Biochemistry.

Microseed matrix screening to improve crystals of yeast cytosine deaminase.

B. Stoddard, G. Ireton, 2004 .

Rational design of α-helical tandem repeat proteins with closed architectures

P. Bradley, D. Baker, B. Stoddard, 2015 .

Homing endonuclease structure and function

B. Stoddard, 2005, Quarterly Reviews of Biophysics.

Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers

B. Stoddard, A. Lambert, H. Kiem, 2017, Nature Communications.

Exploitation of binding energy for catalysis and design

Summer B. Thyme, D. Baker, B. Stoddard, 2009, Nature.

The tertiary structure and domain organization of coagulation factor VIII.

B. Shen, B. Stoddard, Chong-Hwan Chang, 2008, Blood.

Computational redesign of endonuclease DNA binding and cleavage specificity

D. Baker, B. Stoddard, R. Monnat, 2006, Nature.

The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate.

B. Stoddard, A. Mesecar, P. Heath, 1998, Structure.

Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.

D E Koshland, D. Koshland, B. Stoddard, 1997, Science.

Computational Design of Ligand Binding Proteins

Barry L. Stoddard, B. Stoddard, 2016, Methods in Molecular Biology.

Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.

B. Stoddard, R. Monnat, B. Chevalier, 2000, Journal of molecular biology.

Oxidative Inhibition of Human Soluble Catechol-O-methyltransferase*

B. Stoddard, W. W. Parson, Naomi J H Cotton, 2004, Journal of Biological Chemistry.

Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.

B. Stoddard, B. Chevalier, B L Stoddard, 2001, Nucleic acids research.

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.

B. Stoddard, Barry L Stoddard, J. Pelletier, 2004, Nucleic acids research.

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

David Baker, Barry L. Stoddard, Justin Ashworth, 2010, Nucleic acids research.

Homing endonucleases from mobile group I introns: discovery to genome engineering

B. Stoddard, 2014, Mobile DNA.

Calcineurin-immunosuppressor complexes.

B. Stoddard, K. E. Flick, 1996, Current opinion in structural biology.

Control of repeat protein curvature by computational protein design

David Baker, Barry L. Stoddard, Keunwan Park, 2014, Nature Structural &Molecular Biology.

Engineering and functionalization of large circular tandem repeat protein nanoparticles

P. Bradley, B. Shen, B. Stoddard, 2020, Nature Structural & Molecular Biology.

AcrIIA22 is a novel anti-CRISPR that impairs SpyCas9 activity by relieving DNA torsion of target plasmids

B. Stoddard, Kevin J. Forsberg, Harmit S. Malik, 2020 .

Redesign of extensive protein–DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization

B. Stoddard, R. Takeuchi, Michael Choi, 2014, Proceedings of the National Academy of Sciences.

Efficient Modification of the CCR5 Locus in Primary Human T Cells With megaTAL Nuclease Establishes HIV-1 Resistance

B. Stoddard, D. Rawlings, H. Kiem, 2016, Molecular therapy. Nucleic acids.

Efficient Modification of the CCR5 Locus in Primary Human T Cells With megaTAL Nuclease Establishes HIV-1 Resistance

B. Stoddard, D. Rawlings, H. Kiem, 2016, Molecular Therapy: Nucleic Acids.

Millisecond Laue structures of an enzyme–product complex using photocaged substrate analogs

D. Koshland, B. Stoddard, B. Cohen, 1998, Nature Structural Biology.

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.

D. Baker, B. Stoddard, B. Kuhlman, 2006, Journal of molecular biology.

The crystal structure of yeast cytosine deaminase bound to 4(R)-hydroxyl-3,4-dihydropyrimidine at 1.14 angstroms.

B. Stoddard, G. Ireton, M. Black, 2003 .

Optimization of factor VIII replacement therapy: can structural studies help in evading antibody inhibitors?

B. Stoddard, P. C. Spiegel, P. Spiegel, 2002, British journal of haematology.

Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.

B. Shen, B. Stoddard, R. Morgan, 2010, Structure.

Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system

B. Stoddard, L. Doyle, A. Lambert, 2022, Nucleic acids research.

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family

O. Schueler‐Furman, B. Stoddard, S. Pietrokovski, 2009, Nucleic acids research.

Mir for the crystallographers' money

Barry L. Stoddard, Roland K. Strong, Gregory K. Farber, 1992, Nature.

Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.

B. Shen, B. Stoddard, J. Quispe, 2021, Structure.

Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM

B. Shen, B. Stoddard, J. Quispe, 2021, bioRxiv.

Thermodynamics of DNA target site recognition by homing endonucleases

B. Shen, B. Stoddard, Justin Ashworth, 2007, Nucleic acids research.

Can Laue catch Maxwell?: observation of short-lived species by Laue X-ray crystallography

B. Stoddard, D. Ringe, N. Porter, 1992, Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences.

Observation of the light-triggered binding of pyrone to chymotrypsin by Laue x-ray crystallography.

G. Petsko, B. Stoddard, D. Ringe, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Photolysis and deacylation of inhibited chymotrypsin.

G. Petsko, B. Stoddard, D. Ringe, 1990, Biochemistry.

Receptors and transmembrane signaling.

D. Koshland, B. Stoddard, H. Biemann, 1992, Cold Spring Harbor symposia on quantitative biology.

Human fibroblast-derived growth factor is a mitogen and chemoattractant for endothelial cells.

B. Stoddard, D. Connolly, J. Feder, 1987, Biochemical and biophysical research communications.

1,3-Dioxane-4,6-dione-5-carboxamide-based inhibitors of human group IIA phospholipase A: X-ray structure of the complex and interfacial selection of inhibitors from a structural library.

B. Stoddard, M. Gelb, R. Koduri, 1999, Bioorganic & medicinal chemistry letters.

Structures of the rare-cutting restriction endonuclease NotI reveal a novel metal binding fold involved in DNA recognition

B. Stoddard, A. Lambert, Shuang-yong Xu, 2008 .

Restriction endonucleases: one of these things is not like the others

B. Stoddard, E. Galburt, 2000, Nature Structural Biology.

The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive

B. Stoddard, S. Russell, R. Takeuchi, 2013, PloS one.

Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses

B. Stoddard, A. Lambert, A. Greninger, 2017, Protein engineering, design & selection : PEDS.

Direct measurement of diffusion rates in enzyme crystals by video absorbance spectroscopy

B. Stoddard, P. O'Hara, P. Goodwin, 1995 .

Editorial: Alfred Pingoud (1945–2015)

B. Stoddard, A. Jeltsch, P. Friedhoff, 2015, Nucleic acids research.

HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM

B. Stoddard, R. Monnat, B. Chevalier, 2001 .

Crystallization and preliminary X‐ray studies of I‐PpoI: A nuclear, intron‐encoded homing endonuclease from Physarum polycephalum

B. Stoddard, R. Monnat, K. Stephens, 1997, Protein science : a publication of the Protein Society.

DNAbindingandcleavageby thenuclear intron-encoded homingendonuclease IPpo I

B. Stoddard, R. Monnat, M. Jurica, 2022 .

Homing endonucleases: structure, function and evolution

B. Stoddard, M. Jurica, 1999, Cellular and Molecular Life Sciences CMLS.

Crystallization and preliminary x‐ray studies of I‐CreI: a group I intron‐encoded endonuclease from C. reinhardtii

B. Stoddard, R. Monnat, P. Heath, 1997, Proteins.

Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization.

B. Stoddard, R. Takeuchi, Michael Choi, 2015, Methods in molecular biology.

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.

B. Shen, B. Stoddard, A. Lambert, 2016, Structure.

novo design of a fluorescence-activating β-barrel.

Min Yen Lee, Lauren A. Gagnon, M. J. Bick, 2018 .

Effects of D-serine on bacterial D-amino acid transaminase: accumulation of an intermediate and inactivation of the enzyme.

G. Petsko, B. Stoddard, D. Ringe, 1989, Biochemistry.

Crystallization and preliminary X-ray analysis of bacterial cytosine deaminase.

B. Stoddard, G. Ireton, M. Black, 2001, Acta crystallographica. Section D, Biological crystallography.

Purification, crystallization, and preliminary X‐ray studies of 10‐formyltetrahydrofolate synthetase from Clostridia acidici‐urici

B. Stoddard, J. Bolduc, J. Rabinowitz, 1997, Proteins.

Preliminary X-ray data for a D-amino acid amino-transferase from a novel thermophilic Bacillus.

G. Petsko, B. Stoddard, D. Ringe, 1987, Journal of molecular biology.

DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.

B. Stoddard, R. Monnat, M. Jurica, 1998, Molecular cell.

Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo.

B. Stoddard, M. Black, Andressa Ardiani, 2009, Cancer research.

Comparative architecture of transposase and integrase complexes

B. Stoddard, J. Richardson, R. Monnat, 2001, Nature Structural Biology.

Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.

B. Stoddard, Barry L Stoddard, 2011, Structure.

Advances in Engineering Homing Endonucleases for Gene Targeting: Ten Years After Structures

B. Stoddard, R. Monnat, A. Scharenberg, 2007 .

Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE

B. Stoddard, K. Fox, S. Machida, 2021, Nucleic acids research.

Author response: Precise assembly of complex beta sheet topologies from de novo designed building blocks

John F. Hunt, David Baker, Barry L. Stoddard, 2015 .

Structure and activity of two photoreversible cinnamates bound to chymotrypsin.

G A Petsko, G. Petsko, B. Stoddard, 1990, Biochemistry.

Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII.

B. Stoddard, J. Saint-Remy, K. Pratt, 2001, Blood.

Hemophilic factor VIII C1- and C2-domain missense mutations and their modeling to the 1.5-angstrom human C2-domain crystal structure.

K. Fujikawa, B. Shen, B. Stoddard, 2000, Blood.

identification of an inhibitory antibody epitope on the surface of factor VIII Fab complex: κ immunoglobulin G4 - Structure of a factor VIII C2 domain

B. Stoddard, J. Saint-Remy, K. Pratt, 2013 .

Structure of the C2 domain of human factor VIII at 1.5 Å resolution

K. Fujikawa, B. Shen, B. Stoddard, 1999, Nature.

The crystal structure and mutational analysis of human NUDT9.

B. Shen, B. Stoddard, A. Perraud, 2003, Journal of molecular biology.

The 2.1-A resolution structure of iron superoxide dismutase from Pseudomonas ovalis.

Barry L. Stoddard, Dagmar Ringe, Gregory A. Petsko, 1990, Biochemistry.

Trapping reaction intermediates in macromolecular crystals for structural analyses.

B. Stoddard, Barry L. Stoddard, 2001, Methods.

Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-A resolution: a pseudo-Michaelis ternary complex.

D. Koshland, B. Stoddard, A. Dean, 1993, Biochemistry.

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Ryo Takeuchi, David Baker, Joel L Sussman, 2012, Nature chemical biology.

The crystal structure of a bacterial, bifunctional 5, 10 methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase

B. Shen, B. Stoddard, D. Dyer, 1999, Protein science : a publication of the Protein Society.

Purification, crystallization, and preliminary X‐ray studies of a bifunctional 5,10‐methenyl/methylene tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli

B. Stoddard, D. Dyer, J. Rabinowitz, 1997, Proteins.

Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome

Barry L. Stoddard, B. Stoddard, Kevin J. Forsberg, 2019, bioRxiv.

Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity

M. Pogson, B. Stoddard, A. Lambert, 2017, Nucleic acids research.

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

David Baker, Jay Shendure, Barry L. Stoddard, 2013, Nucleic acids research.

The structure of Escherichia coli cytosine deaminase.

Gerry McDermott, G. McDermott, B. Stoddard, 2002, Journal of molecular biology.

Long duration growth of protein crystals in microgravity aboard the MIR space station

B. Stoddard, A. Arrott, R. Strong, 1992 .

The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.

B. Stoddard, G. Ireton, M. Black, 2003, Structure.

Determinants of allosteric activation of yeast pyruvate kinase and identification of novel effectors using computational screening.

C. J. Bond, B. Stoddard, A. Mesecar, 2000, Biochemistry.

Robust computational design, optimization, and structural characterization of retroaldol enzymes

David Baker, Barry L. Stoddard, Eric A. Althoff, 2011 .

Engineering altered protein–DNA recognition specificity

A. Bogdanove, B. Stoddard, Jeffrey C. Miller, 2018, Nucleic acids research.

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity

B. Stoddard, Kevin J. Forsberg, Harmit S. Malik, 2021, bioRxiv.

Editorial: CRISPR in Nucleic Acids Research

B. Stoddard, K. Fox, 2016, Nucleic acids research.

Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI.

Monique Turmel, Claude Lemieux, Raymond J Monnat, 2003, Journal of molecular biology.

Accumulation of Free ADP-ribose from Mitochondria Mediates Oxidative Stress-induced Gating of TRPM2 Cation Channels*

B. Stoddard, A. Perraud, A. Scharenberg, 2005, Journal of Biological Chemistry.

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins

Rommie E. Amaro, Emília P. Barros, Min Yen Lee, 2021, Nature Communications.

Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity

Barry L. Stoddard, Siu-Hong Chan, Shuang-yong Xu, 2010, Nucleic Acids Res..

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.

David Baker, Lindsey Doyle, Nephi Stella, 2018, Protein engineering, design & selection : PEDS.

Computational design of ligand-binding proteins with high affinity and selectivity

David Baker, Barry L. Stoddard, Sagar D. Khare, 2013, Nature.

I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities.

Markus Landthaler, B. Shen, B. Stoddard, 2006, Journal of molecular biology.

Faculty Opinions recommendation of A novel peptidoglycan cross-linking enzyme for a beta-lactam-resistant transpeptidation pathway.

B. Stoddard, 2005 .

Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge

B. Stoddard, A. McGuire, D. Veesler, 2022, bioRxiv.

Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.

B. Stoddard, R. Monnat, Barry L Stoddard, 2007, Biochemistry.

Alteration of enzyme specificity by computational loop remodeling and design

Jasmine L. Gallaher, B. Stoddard, J. Bolduc, 2009, Proceedings of the National Academy of Sciences.

NUDT9, a Member of the Nudix Hydrolase Family, Is an Evolutionarily Conserved Mitochondrial ADP-ribose Pyrophosphatase*

B. Stoddard, K. Rippe, A. Perraud, 2003, The Journal of Biological Chemistry.

Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease

Ryo Takeuchi, Barry L. Stoddard, Raymond J. Monnat, 2009, Proceedings of the National Academy of Sciences.

A synthetic sex ratio distortion system for the control of the human malaria mosquito

B. Stoddard, L. Doyle, A. Burt, 2014, Nature Communications.

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins.

Erin L. Doyle, Daniel F Voytas, A. Bogdanove, 2013, Trends in cell biology.

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

David Baker, Patrick Danaher, Barry L. Stoddard, 2012, Nucleic acids research.

Laue crystallography: coming of age

B. Stoddard, Z. Ren, K. Moffat, 1999 .

The structural basis of mRNA recognition and binding by eukaryotic pseudouridine synthase PUS1

B. Stoddard, L. Doyle, Ivan R. Corrêa, 2021, bioRxiv.

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

B. Stoddard, A. Lambert, J. Hallinan, 2020, Structure.

The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease.

B. Shen, B. Stoddard, Brett K. Kaiser, 2009, Structure.

Breaking up is hard to do

Shmuel Pietrokovski, Barry L. Stoddard, B. Stoddard, 1998, Nature Structural Biology.

Tapping natural reservoirs of homing endonucleases for targeted gene modification

Ryo Takeuchi, Kyle Jacoby, Russell J. Dickson, 2011, Proceedings of the National Academy of Sciences.

Biocontainment of genetically modified organisms by synthetic protein design

Ryo Takeuchi, George M. Church, Barry L. Stoddard, 2015, Nature.

Substitution of glutamine for lysine at the pyridoxal phosphate binding site of bacterial D-amino acid transaminase. Effects of exogenous amines on the slow formation of intermediates.

B. Stoddard, D. Ringe, S. Futaki, 1990, Journal of Biological Chemistry.

DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI

Barry L. Stoddard, Raymond J. Monnat, Melissa S. Jurica, 1998, Nature.

Catalytic mechanisms of restriction and homing endonucleases.

B. Stoddard, Barry L Stoddard, Eric A Galburt, 2002, Biochemistry.

De novo design of a fluorescence-activating β-barrel

William Sheffler, Binchen Mao, Barry L. Stoddard, 2018, Nature.

Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.

B. Stoddard, G. Wilson, J. Pelletier, 2002, Structure.

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

Philip Bradley, P. Bradley, A. Bogdanove, 2012, Science.

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

B. Stoddard, W. Dynan, K. Fox, 2013, Nucleic acids research.

Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family

B. Stoddard, S. Pietrokovski, G. K. Taylor, 2011, Nucleic acids research.

Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI

B. Shen, B. Stoddard, Shuang-yong Xu, 2011, Nucleic acids research.

DNA binding and cleavage by the HNH homing endonuclease I-HmuI.

Markus Landthaler, B. Shen, B. Stoddard, 2004, Journal of molecular biology.

Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.

B. Stoddard, A. Lambert, Amanda Nga-Sze Mak, 2010, Structure.

The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD‐(D/E)‐XK motif

B. Stoddard, R. P. Bonocora, D. Shub, 2007, The EMBO journal.

Social networking between mobile introns and their host genes

B. Stoddard, M. Belfort, 2010, Molecular microbiology.

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

David Baker, Barry L. Stoddard, Bruno E. Correia, 2014, Cell.

Rational design of alpha-helical tandem repeat proteins with closed architectures

David Baker, Barry L. Stoddard, Fabio Parmeggiani, 2015, Nature.

Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor

B. Shen, B. Stoddard, L. Doyle, 2023, Nucleic acids research.

Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His–Cys box homing endonucleases

B. Stoddard, N. Nomura, Y. Nomura, 2008, Nucleic acids research.

Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.

B. Shen, B. Stoddard, A. Lambert, 2008, Structure.

Homology modeling and mutational analysis of Ho endonuclease of yeast.

B. Stoddard, M. Jurica, Anna Bakhrat, 2004, Genetics.

PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks.

B. Stoddard, R. Monnat, M. Metzger, 2013, DNA repair.

Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference.

B. Stoddard, G. Ireton, M. Black, 2004, Biochemistry.

Homing endonuclease structureand function

B. Stoddard, 2005 .

Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening.

B. Stoddard, 1996, Pharmacology & therapeutics.

Retargeting: an unrecognized consideration in endonuclease-based gene drive biology

B. Stoddard, R. Monnat, A. Scharenberg, 2016, bioRxiv.

Precise assembly of complex beta sheet topologies from de novo designed building blocks

David Baker, Gaetano T Montelione, Frank DiMaio, 2015, eLife.

Microseed matrix screening to improve crystals of yeast cytosine deaminase.

B. Stoddard, G. Ireton, Barry L Stoddard, 2004, Acta crystallographica. Section D, Biological crystallography.

The effect of increasing numbers of repeats on TAL effector DNA binding specificity

A. Bogdanove, B. Stoddard, L. Doyle, 2017, Nucleic acids research.

Sampling and energy evaluation challenges in ligand binding protein design

David Baker, Barry L. Stoddard, Hahnbeom Park, 2017, Protein science : a publication of the Protein Society.

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation

Michael T. Certo, B. Stoddard, A. Scharenberg, 2008, Nucleic acids research.

UC Santa Cruz UC Santa Cruz Previously Published Works

B. Stoddard, W. Scott, W. Scott, 2003 .

Transmembrane signalling and the aspartate receptor.

B. Stoddard, W. Scott, W. Scott, 1994, Structure.

Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system

B. Stoddard, L. Doyle, A. Lambert, 2022, bioRxiv.

Identification and characterization of BrxR as a regulatory gene in the BREX phage restriction system

B. Stoddard, L. Doyle, A. Lambert, 2021 .

Caged NADP and NAD. Synthesis and characterization of functionally distinct caged compounds.

D. Koshland, B. Stoddard, B. Cohen, 1997, Biochemistry.

Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms

B. Stoddard, G. K. Taylor, 2012, Nucleic acids research.

Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.

D. Koshland, B. Stoddard, 1993, Biochemistry.

Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.

B. Stoddard, Stefan Pellenz, Lei Zhao, 2009, Journal of molecular biology.

Caught in a chemical trap

B. Stoddard, 1996, Nature Structural Biology.

Combining Laue diffraction and molecular dynamics to study enzyme intermediates

B. Stoddard, P. Bash, A. Dean, 1996, Nature Structural Biology.

The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.

B. Shen, B. Stoddard, A. Lambert, 2016, Journal of molecular biology.

High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display

Barry L. Stoddard, Lindsey Doyle, Christopher G. Hubert, 2009, Nucleic acids research.

Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins

Barry L. Stoddard, Umut Y. Ulge, Raymond J. Monnat, 2009, Nucleic acids research.

Coevolution of a homing endonuclease and its host target sequence.

B. Stoddard, M. Scalley‐Kim, Barry L Stoddard, 2007, Journal of molecular biology.

Homing endonuclease I-CreI derivatives with novel DNA target specificities

Barry L. Stoddard, B. Stoddard, L. Seligman, 2006, Nucleic acids research.

The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold.

B. Stoddard, B. Chevalier, C. Lemieux, 2006, Structure.

Isolation and characterization of new homing endonuclease specificities at individual target site positions.

B. Stoddard, R. Monnat, M. Chadsey, 2004, Journal of molecular biology.

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.

B. Stoddard, R. Waring, J. Bolduc, 2003, Genes & development.

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Michael J MacCoss, David Baker, Alex Zelter, 2016, eLife.

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.

Liang Tong, Vikram Khipple Mulligan, Barry L. Stoddard, 2013, Journal of the American Chemical Society.

Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.

David Baker, Donald Hilvert, Eric A. Althoff, 2011, Journal of molecular biology.

Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces

P. Bradley, B. Shen, B. Stoddard, 2021, Communications Biology.

Increased Diels-Alderase Activity through Foldit Player Guided Backbone Remodeling

David Baker, Zoran Popovic, Jacob B. Bale, 2012, Nature Biotechnology.

Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli.

D E Koshland, D. Koshland, B. Stoddard, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers

B. Stoddard, A. Lambert, H. Kiem, 2017, Nature Communications.

Surface-exposed Hemophilic Mutations across the Factor VIII C2 Domain Have Variable Effects on Stability and Binding Activities*

B. Stoddard, P. Murphy, P. Spiegel, 2004, Journal of Biological Chemistry.

Disruption of protein-membrane binding and identification of small-molecule inhibitors of coagulation factor VIII.

B. Stoddard, Shari M. Kaiser, J. Simon, 2004, Chemistry & biology.

Deletion of residue Ala2201 in the Factor VIII C2 domain results in mild haemophilia A and destroys a major antigenic determinant recognized by Factor VIII inhibitor antibodies

B. Stoddard, J. Vermylen, K. Peerlinck, 2001 .

Engineering and functionalization of large circular tandem repeat protein nanoparticles

P. Bradley, B. Shen, B. Stoddard, 2020, Nature Structural & Molecular Biology.

TAL effectors: function, structure, engineering and applications.

P. Bradley, A. Bogdanove, B. Stoddard, 2013, Current opinion in structural biology.

New results using Laue diffraction and time-resolved crystallography.

B. Stoddard, 1998, Current opinion in structural biology.

Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking

B. Stoddard, Y. Hsia, Andrew J. Borst, 2023, bioRxiv.

Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI

B. Stoddard, R. Morgan, Y. Luyten, 2023, Nucleic acids research.

Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI

P. Bradley, B. Shen, B. Stoddard, 2018, Nucleic acids research.

Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease.

Monique Turmel, Christian Otis, Claude Lemieux, 2004, Biochemistry.

A novel endonuclease mechanism directly visualized for I-PpoI

B. Stoddard, R. Monnat, B. Chevalier, 1999, Nature Structural Biology.

DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target

B. Shen, B. Stoddard, G. Wilson, 2016, Nucleic acids research.

Structure and dynamics of transmembrane signaling by the Escherichia coli aspartate receptor.

D. Koshland, B. Stoddard, J. Bui, 1992, Biochemistry.

De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs

Justin R. Caram, Ralph A. Cacho, B. Stoddard, 2023, Research square.

Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space

Michael T. Certo, B. Shen, B. Stoddard, 2012, Nucleic acids research.

Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases

Sarah K. Baxter, B. Stoddard, R. Monnat, 2007, Nucleic acids research.

The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites

Barry L. Stoddard, Raymond J. Monnat, B. Stoddard, 2001, Nature Structural Biology.

The LAGLIDADG Homing Endonuclease Family

B. Stoddard, R. Monnat, B. Chevalier, 2005 .

Design of apparatus and experiments to determine the effect of microgravity on the crystallization of biological macromolecules using the MIR spacestation

G. Petsko, B. Stoddard, A. Arrott, 1991 .

Telomeres: Structure of a chromosome's aglet

B. Stoddard, D. Gottschling, 1999, Current Biology.

Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template

B. Stoddard, A. Miller, M. Metzger, 2010, Nucleic acids research.

The structural basis of mRNA recognition and binding by eukaryotic pseudouridine synthase PUS1

B. Stoddard, L. Doyle, Ivan R. Corrêa, 2021, bioRxiv.

DNA recognition and transcriptional regulation by the WhiA sporulation factor

B. Stoddard, Brett K. Kaiser, B. Kaiser, 2011, Scientific reports.

Editorial: Nucleic Acids Research and Nucleic Acid Therapeutics

B. Stoddard, A. Khvorova, W. Dynan, 2018, Nucleic acids research.

Stepwise design of pseudosymmetric protein hetero-oligomers

B. Stoddard, L. Carter, V. Wysocki, 2023, bioRxiv.

Computational redesign of endonuclease DNA binding and cleavage specificity

Ashworth, B. Stoddard, R. Monnat, 2006 .

Structure of TAL effector PthXo1 bound to its DNA target

P. Bradley, A. Bogdanove, B. Stoddard, 2012 .

Computational redesign of endonuclease DNA binding and cleavage specificity

B. Stoddard, R. Monnat, J. Havranek, 2006, Nature.

Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis.

C. J. Bond, B. Stoddard, P. Heath, 2000, Acta crystallographica. Section D, Biological crystallography.

native BbvCI A2B2 tetramer at low resolution

B. Shen, B. Stoddard, L. Doyle, 2018 .

Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy.

B. Stoddard, G. Ireton, M. Black, 2004, Protein engineering, design & selection : PEDS.

Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity

B. Stoddard, Shuang-yong Xu, S. Chan, 2010, Nucleic Acids Res..

Direct measurement of reactivity in the protein crystal by steady-state kinetic studies.

B. Stoddard, G. Farber, B. Stoddard, 1995, Structure.

Dynamic Processes in Proteins by X-Ray Diffraction

G. Petsko, J. Hajdu, B. Stoddard, 1990 .

Mind your B's and R's: bacterial chemotaxis, signal transduction and protein recognition.

B. Stoddard, M. Jurica, B L Stoddard, 1998, Structure.

LAHEDES: the LAGLIDADG homing endonuclease database and engineering server

Barry L. Stoddard, Gregory K. Taylor, Abigail R. Lambert, 2012, Nucleic Acids Res..

Combinatorial thinking in chemistry and biology.

B. Stoddard, J. Ellman, J. Wells, 1997, Proceedings of the National Academy of Sciences of the United States of America.

The structure of iron superoxide dismutase from Pseudomonas ovalis complexed with the inhibitor azide.

G A Petsko, G. Petsko, B. Stoddard, 1990, Protein engineering.