Thomas Kodadek

Scripps Florida, The Scripps Research Institute

Affiliated withThe Scripps Research Institute

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 5	2014

Other Publications

Article	Year
Toward synthetic transcription activators: recruitment of transcription factors to DNA by a PNA-peptide chimera. Journal of the American Chemical Society\| PubMed ID: 11866581	2002
Magnetic resonance imaging detects a specific peptide-protein binding event. Journal of the American Chemical Society\| PubMed ID: 11929234	2002
Recruitment of a 19S proteasome subcomplex to an activated promoter. Science (New York, N.Y.)\| PubMed ID: 11964484	2002
Development of protein-detecting microarrays and related devices. Trends in biochemical sciences\| PubMed ID: 12069789	2002
Removal of impurities from transcription factor preparations that alter their DNA-binding properties. Nucleic acids research\| PubMed ID: 12177316	2002
Physical association of the APIS complex and general transcription factors. Biochemical and biophysical research communications\| PubMed ID: 12200147	2002
Inhibition of proteolysis and other posttranslational modifications with substrate-targeted inhibitors. Biopolymers\| PubMed ID: 12325163	2002
A nonproteolytic function of the 19S regulatory subunit of the 26S proteasome is required for efficient activated transcription by human RNA polymerase II. Biochemistry\| PubMed ID: 12379122	2002
Microwave-assisted solid-phase synthesis of peptoids. Organic letters\| PubMed ID: 12423085	2002
Protein affinity labeling mediated by genetically encoded peptide tags. Angewandte Chemie (International ed. in English)\| PubMed ID: 12491432	2002
Immobilized peptides as high-affinity capture agents for self-associating proteins. Chemistry & biology\| PubMed ID: 12670539	2003
Mixed-element capture agents: a simple strategy for the construction of synthetic, high-affinity protein capture ligands. Journal of the American Chemical Society\| PubMed ID: 12903996	2003
Transcription activation by a PNA-peptide chimera in a mammalian cell extract. Chemistry & biology\| PubMed ID: 14583257	2003
Isolation of protein ligands from large peptoid libraries. Journal of the American Chemical Society\| PubMed ID: 14611236	2003
Quantum dots as a visual aid for screening bead-bound combinatorial libraries. Chembiochem : a European journal of chemical biology\| PubMed ID: 14613120	2003
Using oxidative crosslinking and proximity labeling to quantitatively characterize protein-protein and protein-Peptide complexes. Chemistry & biology\| PubMed ID: 14652079	2003
Peptides as modulators of enzymes and regulatory proteins. Methods (San Diego, Calif.)\| PubMed ID: 15003603	2004
Photolithographic synthesis of peptoids. Journal of the American Chemical Society\| PubMed ID: 15053581	2004
Physical and functional association of RNA polymerase II and the proteasome. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15069196	2004
Target identification in chemical genetics: the (often) missing link. Chemistry & biology\| PubMed ID: 15157870	2004
Toward a general chemical method for rapidly mapping multi-protein complexes. Journal of proteome research\| PubMed ID: 15253422	2004
Transformation of low-affinity lead compounds into high-affinity protein capture agents. Chemistry & biology\| PubMed ID: 15324814	2004
Periodate-triggered cross-linking of DOPA-containing peptide-protein complexes. Journal of the American Chemical Society\| PubMed ID: 15366882	2004
Synthetic molecules as antibody replacements. Accounts of chemical research\| PubMed ID: 15379586	2004
The potential of protein-detecting microarrays for clinical diagnostics. Advances in clinical chemistry\| PubMed ID: 15521193	2004
Photolithographic synthesis of cyclic peptide arrays using a differential deprotection strategy. Chemical communications (Cambridge, England)\| PubMed ID: 15672142	2005
Genomic studies of transcription factor-DNA interactions. Current opinion in chemical biology\| PubMed ID: 15701451	2005
Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events. Trends in pharmacological sciences\| PubMed ID: 15808346	2005
A high-throughput assay for assessing the cell permeability of combinatorial libraries. Nature biotechnology\| PubMed ID: 15908941	2005
A potent transactivation domain mimic with activity in living cells. Journal of the American Chemical Society\| PubMed ID: 15941237	2005
Protein "fingerprinting" in complex mixtures with peptoid microarrays. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16123137	2005
NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein. Biochemistry\| PubMed ID: 16285728	2005
The proteasomal ATPase complex is required for stress-induced transcription in yeast. Nucleic acids research\| PubMed ID: 16517940	2006
Widespread, but non-identical, association of proteasomal 19 and 20 S proteins with yeast chromatin. The Journal of biological chemistry\| PubMed ID: 16837462	2006
Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads. Molecular bioSystems\| PubMed ID: 16880920	2006
Simple reporter gene-based assays for hairpin poly(amide) conjugate permeability and DNA-binding activity in living cells. Molecular bioSystems\| PubMed ID: 16880996	2005
Identification of Gal4 activation domain-binding proteins in the 26S proteasome by periodate-triggered cross-linking. Molecular bioSystems\| PubMed ID: 16881005	2005
Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo. Nature\| PubMed ID: 16929306	2006
Keeping transcriptional activators under control. Cell\| PubMed ID: 17055428	2006
Chemistry of periodate-mediated cross-linking of 3,4-dihydroxylphenylalanine-containing molecules to proteins. Journal of the American Chemical Society\| PubMed ID: 17117875	2006
The role of the proteasomal ATPases and activator monoubiquitylation in regulating Gal4 binding to promoters. Genes & development\| PubMed ID: 17167105	2007
Isolation and characterization of coactivator-binding peptoids from a combinatorial library. Molecular bioSystems\| PubMed ID: 17216038	2006
Introduction to monitoring and manipulating signaling networks. Molecular bioSystems\| PubMed ID: 17216040	2006
Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival. Molecular bioSystems\| PubMed ID: 17216044	2006
Quantitative evaluation of the relative cell permeability of peptoids and peptides. Journal of the American Chemical Society\| PubMed ID: 17283989	2007
A cell-permeable synthetic transcription factor mimic. Angewandte Chemie (International ed. in English)\| PubMed ID: 17351994	2007
A convenient, high-throughput assay for measuring the relative cell permeability of synthetic compounds. Nature protocols\| PubMed ID: 17401333	2007
Design and synthesis of a cell-permeable synthetic transcription factor mimic. Journal of combinatorial chemistry\| PubMed ID: 17530904	2007
Identification of a peptoid inhibitor of the proteasome 19S regulatory particle. Journal of the American Chemical Society\| PubMed ID: 17536803	2007
Quantitative comparison of the relative cell permeability of cyclic and linear peptides. Chemistry & biology\| PubMed ID: 17584614	2007
Label transfer chemistry for the characterization of protein-protein interactions. Journal of the American Chemical Society\| PubMed ID: 17894490	2007
Dynamics of the hypoxia-inducible factor-1-vascular endothelial growth factor promoter complex. The Journal of biological chemistry\| PubMed ID: 17916562	2007
Periodate-triggered cross-linking reveals Sug2/Rpt4 as the molecular target of a peptoid inhibitor of the 19S proteasome regulatory particle. Journal of the American Chemical Society\| PubMed ID: 17929816	2007
The neurohormone orexin stimulates hypoxia-inducible factor-1 activity. Genes & development\| PubMed ID: 18006690	2007
Characterization of proteomic and metabolomic responses to dietary factors and supplements. The Journal of nutrition\| PubMed ID: 18029500	2007
A general system for evaluating the efficiency of chromophore-assisted light inactivation (CALI) of proteins reveals Ru(II) tris-bipyridyl as an unusually efficient "warhead". Molecular bioSystems\| PubMed ID: 18075676	2008
The detection limit of a Gd3+-based T1 agent is substantially reduced when targeted to a protein microdomain. Magnetic resonance imaging\| PubMed ID: 18234462	2008
Rapid identification of the pharmacophore in a peptoid inhibitor of the proteasome regulatory particle. Chemical communications (Cambridge, England)\| PubMed ID: 18292891	2008
Activation domain-dependent monoubiquitylation of Gal4 protein is essential for promoter binding in vivo. The Journal of biological chemistry\| PubMed ID: 18326036	2008
Use of peptide analogue diversity library beads for increased depth of proteomic analysis: application to cerebrospinal fluid. Journal of proteome research\| PubMed ID: 18357977	2008
A peptoid "antibody surrogate" that antagonizes VEGF receptor 2 activity. Journal of the American Chemical Society\| PubMed ID: 18386897	2008
High-throughput evaluation of relative cell permeability between peptoids and peptides. Bioorganic & medicinal chemistry\| PubMed ID: 18490170	2008
A peptoid antagonist of VEGF receptor 2 recognizes a 'hotspot' in the extracellular domain distinct from the hormone-binding site. Bioorganic & medicinal chemistry\| PubMed ID: 18501615	2008
Physical and functional interactions of monoubiquitylated transactivators with the proteasome. The Journal of biological chemistry\| PubMed ID: 18515799	2008
Biochemistry: Molecular cloaking devices. Nature\| PubMed ID: 18548057	2008
Proteomes take the electrophilic bait. Nature chemical biology\| PubMed ID: 18560426	2008
The pharmacophore of a peptoid VEGF receptor 2 antagonist includes both side chain and main chain residues. Bioorganic & medicinal chemistry letters\| PubMed ID: 18653335	2008
Rise of the machines: Bruce Alberts and the biochemistry of multi-protein complexes. Molecular bioSystems\| PubMed ID: 18931779	2008
Phosphorylation of the Gal4 DNA-binding domain is essential for activator mono-ubiquitylation and efficient promoter occupancy. Molecular bioSystems\| PubMed ID: 18931787	2008
Encoded combinatorial libraries for the construction of cyclic peptoid microarrays. Chemical communications (Cambridge, England)\| PubMed ID: 19009054	2008
Selective toxin sequestrants for the treatment of bacterial infections. Journal of the American Chemical Society\| PubMed ID: 19351156	2009
Rapid identification of improved protein ligands using peptoid microarrays. Bioorganic & medicinal chemistry letters\| PubMed ID: 19380225	2009
Genome-wide analysis of chromatin regulation by cocaine reveals a role for sirtuins. Neuron\| PubMed ID: 19447090	2009
Peptoids as potential therapeutics. Current opinion in molecular therapeutics\| PubMed ID: 19479663	2009
Imipramine treatment and resiliency exhibit similar chromatin regulation in the mouse nucleus accumbens in depression models. The Journal of neuroscience : the official journal of the Society for Neuroscience\| PubMed ID: 19535594	2009
Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides. Journal of medicinal chemistry\| PubMed ID: 19610652	2009
Non-proteolytic regulation of p53-mediated transcription through destabilization of the activator.promoter complex by the proteasomal ATPases. The Journal of biological chemistry\| PubMed ID: 19846554	2009
The hydrophobic patch of ubiquitin is required to protect transactivator-promoter complexes from destabilization by the proteasomal ATPases. Nucleic acids research\| PubMed ID: 19939937	2010
Isolation of antagonists of antigen-specific autoimmune T cell proliferation. Chemistry & biology\| PubMed ID: 19942136	2009
No Splicing, no dicing: non-proteolytic roles of the ubiquitin-proteasome system in transcription. The Journal of biological chemistry\| PubMed ID: 19955182	2010
Rapid identification of orexin receptor binding ligands using cell-based screening accelerated with magnetic beads. Molecular bioSystems\| PubMed ID: 20024071	2010
Seamless bead to microarray screening: rapid identification of the highest affinity protein ligands from large combinatorial libraries. Chemistry & biology\| PubMed ID: 20142039	2010
Rethinking screening. Nature chemical biology\| PubMed ID: 20154660	2010
Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates. Nature chemical biology\| PubMed ID: 20228793	2010
Chemistry and biology of orexin signaling. Molecular bioSystems\| PubMed ID: 20532299	2010
The interface of chemical biology and the nervous system (related to the NIDA Chemical Genomics Symposium). Molecular bioSystems\| PubMed ID: 20582378	2010
Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation. Cancer research\| PubMed ID: 20663904	2010
GU81, a VEGFR2 antagonist peptoid, enhances the anti-tumor activity of doxorubicin in the murine MMTV-PyMT transgenic model of breast cancer. BMC cancer\| PubMed ID: 20673348	2010
Development of antibody surrogates for the treatment of cancers and autoimmune disease. Current opinion in chemical biology\| PubMed ID: 20674470	2010
Synthetic receptors with antibody-like binding affinities. Current opinion in chemical biology\| PubMed ID: 20674471	2010
MRI detection of VEGFR2 in vivo using a low molecular weight peptoid-(Gd)8-dendron for targeting. Journal of the American Chemical Society\| PubMed ID: 20795620	2010
Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening. Cell\| PubMed ID: 21215375	2011
Protein binding: Antibody surrogates click into place. Nature chemistry\| PubMed ID: 21378844	2009
The rise, fall and reinvention of combinatorial chemistry. Chemical communications (Cambridge, England)\| PubMed ID: 21701754	2011
Peptoid ligands that bind selectively to phosphoproteins. Bioorganic & medicinal chemistry letters\| PubMed ID: 21742492	2011
Acyl hydrazides as peptoid sub-monomers. Chemical communications (Cambridge, England)\| PubMed ID: 21892506	2011
PDZ dimerization brings proteins together. Chemistry & biology\| PubMed ID: 21944744	2011
Expanded polyglutamine-binding peptoid as a novel therapeutic agent for treatment of Huntington's disease. Chemistry & biology\| PubMed ID: 21944750	2011
A biomimetic polyketide-inspired approach to small-molecule ligand discovery. Nature chemistry\| PubMed ID: 22270625	2012
Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries. ACS combinatorial science\| PubMed ID: 22320121	2012
On-Bead Two-Color (OBTC) Cell Screen for Direct Identification of Highly Selective Cell Surface Receptor Ligands. Current protocols in chemical biology\| PubMed ID: 22582145	2012
A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron letters\| PubMed ID: 22736872	2012
Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9. Chembiochem : a European journal of chemical biology\| PubMed ID: 22907802	2012
Submonomer synthesis of a hybrid peptoid-azapeptoid library. ACS combinatorial science\| PubMed ID: 22958123	2012
Synthesis of libraries of peptidomimetic compounds containing a 2-oxopiperazine unit in the main chain. Organic & biomolecular chemistry\| PubMed ID: 23440085	2013
Discovery of peptoid ligands for anti-aquaporin 4 antibodies. Chemistry & biology\| PubMed ID: 23521793	2013
Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides. Chemistry & biology\| PubMed ID: 23521794	2013
Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry. Journal of the American Society for Mass Spectrometry\| PubMed ID: 23636859	2013
Advances in blood-based protein biomarkers for Alzheimer's disease. Alzheimer's research & therapy\| PubMed ID: 23659521	2013
Features of modularly assembled compounds that impart bioactivity against an RNA target. ACS chemical biology\| PubMed ID: 24032410	2013
A jack of all trades to combat drug-resistant Gram-negative bacteria. Chemistry & biology\| PubMed ID: 24210003	2013
A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions. ACS chemical biology\| PubMed ID: 24245981	2014
Discovery of biomarkers for systemic lupus erythematosus using a library of synthetic autoantigen surrogates. Journal of immunological methods\| PubMed ID: 24269750	2014
Discovery Of An Orexin Receptor Positive Potentiator. Chemical science (Royal Society of Chemistry : 2010)\| PubMed ID: 24409338	2010
Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS combinatorial science\| PubMed ID: 24749624	2014