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Networks of bZIP protein-protein interactions diversified over a billion years of evolution Aaron W. Reinke, Jiyeon Baek, Orr Ashenberg, Amy E. Keating Science, 2013 [PMID: 23661758] [Full Text] |
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Multistate Protein Design Using CLEVER and CLASSY Christopher Negron, and Amy E. Keating Methods in Enzymology, 2013;523:171-90.[PMID: 23422430] |
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Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening Sanjib Dutta, T. Scott Chen, and Amy E. Keating ACS Chemical Biology, 2013 (In Press) [PMID: 23363053] |
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Helix Bundle Loops Determine Whether Histidine Kinases Autophosphorylate in Cis or in Trans Orr Ashenberg, Amy E. Keating, and Michael T. Laub Journal of Molecular Biology, 2013 (In Press) [PMID: 23333741] |
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bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans Wen-Bing Yin, Aaron W. Reinke, Melinda Szilágyi, Tamás Emri, Yi-Ming Chiang, Amy E. Keating, István Pócsi, Clay C. C. Wang and Nancy P. Keller Microbiology, 2013 Jan;159(Pt 1):77-88 [PMID: 23154967] |
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Structure-based redesign of the binding specificity of anti-apoptotic Bcl-x(L) T. Scott Chen, Hector Palacios, and Amy E. Keating Journal of Molecular Biology, 2013 Jan 9;425(1):171-85 [PMID: 23154169] |
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In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2 Nir London, Stefano Gullá, Amy E. Keating, and Ora Schueler-Furman Biochemistry, 2012 Jul 24;51(29):5841-50 [PMID: 22702834] |
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Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure Joe DeBartolo, Sanjib Dutta, Lothar Reich, and Amy E. Keating Journal of Molecular Biology, 2012 Sep 7;422(1):124-44 [PMID: 22617328] |
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Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods T. Scott Chen, and Amy E. Keating Protein Science, 2012 doi:10.1002/pro.2096. PMID: 22593041 |
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The SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains K. Evan Thompson, Caleb J. Bashor, Wendell A. Lim & Amy E. Keating ACS Synthetic Biology, 2012 Apr 20;1(4):118-129. PMID: 22558529 |
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Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone Jason Trigg, Karl Gutwin, Amy E. Keating & Bonnie Berger PLoS One, 2011 6(8):e23519. PMID: 21901122 |
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Determinants of homodimerization specificity in histidine kinases. Orr Ashenberg, Kathryn Rozen-Gagnon, Michael T. Laub, Amy E. Keating Journal of Molecular Biology, 2011 Oct;413(1):222-35. PMID: 21854787 |
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Design of Peptide Inhibitors that Bind the bZIP Domain of Epstein-Barr Virus protein BZLF1 T. Scott Chen, Aaron W. Reinke and Amy E. Keating Journal of Molecular Biology, 2011 Apr;408(2), 304–320 PMID: 21354428 |
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Protein Binding Specificity versus Promiscuity Gideon Schreiber & Amy E. Keating Current Opinion in Structural Biology, 2011 Feb; 21(1):50-61 PMID: 21071205 |
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Identifying and reducing error in cluster expansion approximations of protein energies Seungsoo Hahn, Orr Asherberg, Gevorg Grigoryan, Amy E. Keating Journal of Computational Chemistry, 2010 Dec;31(16):2900-14. PMID: 20602445 |
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The MCL-1 BH3 Helix is an Exclusive MCL-1 inhibitor and Apoptosis Sensitizer Michelle L. Stewart, Emiko Fire, Amy E. Keating, Loren D. Walensky Nature Chemical Biology, 2010 Aug;6(8):595-601. PMID: 20562877 |
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A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering Aaron W. Reinke, Robert A. Grant, Amy E. Keating. J Am Chem Soc. 2010 May 5;132(17):6025-31.PMID: 20387835 |
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Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-x(L). Sanjib Dutta, Stefano Gullá, T Scott Chen, Emiko Fire, Robert A. Grant, Amy E. Keating. J Mol Biol. 2010 May 21;398(5):747-62. PMID: 20363230 |
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Specific coiled-coil interactions contribute to a global model of the structure of the spindle pole body Nora Zizlsperger, Amy E. Keating J Struct Biol. 170(2):246-56.(2010) Epub 2010 Feb 6. PMID: 20139001 |
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Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays Aaron W. Reinke, Gevorg Grigoryan, Amy E. Keating Biochemistry 49(9):1985-97. (2010) PMID: 20102225 |
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Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes Emiko Fire, Stefano Gulla, Robert Grant, Amy E. Keating Protein science 19(3):507-19. (2010) PMID: 20066663 |
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Design of protein-interaction specificity gives selective bZIP-binding peptides Gevorg Grigoryan, Aaron W. Reinke, Amy E. Keating Nature, 458, 859-864 (2009) |
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Cluster expansion models for flexible-backbone protein energetics James R. Apgar, Seungsoo Hahn, Gevorg Grigoryan, Amy E. Keating Journal of Computational Chemistry 30, 2402-13 (2009) |
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X-ray vs. NMR structures as templates for computational protein design Michael Schneider, Xiaoran Fu, Amy E. Keating Proteins 77, 97-110 (2009) |
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A computationally guided protein-interaction screen uncovers coiled-coil interactions involved in vesicle-mediated transport Hong Zhang, Jinan Chen, Yongqiang Wang, Lin Peng, Xiaoxi Dong, Yi Lu, Amy E. Keating, Taijiao Jiang Journal of Molecular Biology 392, 228-241 (2009) |
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Analysis of coiled-coil interactions between core proteins of the spindle pole body Nora Zizlsperger, Vladimir N. Malashkevich, Shirin Pillay, and Amy E. Keating Biochemistry 47, 11858-68 (2008) |
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Structural specificity in coiled-coil interactions Gevorg Grigoryan and Amy E Keating Current Opinion in Structural Biology 18, 477-483 (2008) |
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Predicting helix orientation for coiled-coil dimers James R. Apgar, Karl N. Gutwin, and Amy E. Keating PROTEINS: Structure, Function, Bioinformatics 72, 1048-1065 (2008) [Abstract] [PDF] (MIT access only) |
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Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. Xiaoran Fu, James R. Apgar, Amy E. Keating Journal of Molecular Biology 371, 1099-117 (2007) |
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Computing van der Waals energies in the context of the rotamer approximation Gevorg Grigoryan, Alejandro Ochoa, Amy E. Keating PROTEINS: Structure, Function, Bioinformatics , 68(4): 863 - 878 (6 Jun 2007). [Abstract] [PDF] (MIT access only) |
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Ultra-fast Evaluation of Protein Energies Directly from Sequence Gevorg Grigoryan, Fei Zhou, Steve R Lustig, Gerbrand Ceder, Dane Morgan, Amy E. Keating PLoS Computational Biology 2(6), e63 (June 2006) |
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Structure-based prediction of bZIP partnering specificity Gevorg Grigoryan and Amy E. Keating J. Mol. Biol. 355, 1125-1142 (3 February, 2006) [PDF] (MIT access only) [Abstract] (free access) |
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Paircoil2: Improved Prediction of Coiled Coils from Sequence Andrew V. McDonnell, Taijiao Jiang, Amy E. Keating and Bonnie Berger Bioinformatics 22(3), 356-8 (2006) paper (free access) click here for Paircoil2 web site |
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Orientation and Oligomerization Specificity of the Bcr Coiled-Coil Oligomerization Domain Christina M. Taylor and Amy E. Keating Biochemistry 44(49), 16246-56 (13 December, 2005) [PDF] [HTML] (MIT access only) [Abstract] (free access) |
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Coarse-Graining Protein Energetics in Sequence Variables Fei Zhou, Gevorg Grigoryan, Steve R. Lustig, Amy E. Keating, Gerbrand Ceder, and Dane Morgan Physical Review Letters 95, 148103 (September 30, 2005) |
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AVID: An integrative framework for discovering functional relationships among proteins Taijiao Jiang and Amy E Keating BMC Bioinformatics 6, 136 (2005) paper at BMC Bioinformatics (free access) AVID Server |
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Design of a Heterospecific, Tetrameric, 21-Residue Miniprotein with Mixed α/ß Structure Mayssam H. Ali, Christina M. Taylor, Gevorg Grigoryan, Karen N. Allen, Barbara Imperiali, and Amy E. Keating Structure 13(2), 225 - 234 (2005) |
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Predicting Specificity in bZIP Coiled-Coil Protein Interactions Jessica H. Fong, Amy E. Keating and Mona Singh Genome Biology 5, R11 (2004) |
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Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays John R. S. Newman and Amy E. Keating Science 300, 2097- 2101 (2003) paper at Science (free access to this paper only) |
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The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains. Thomas A. Keating, C. Gary Marshall, Christopher T. Walsh and Amy E. Keating Nature Structure Biology 9, 22-526 (2002) paper at NSB website (susbscription required for full-text access) |
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Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Amy E. Keating, Valdimir N. Malashkevich, Bruce Tidor and Peter S. Kim Proceedings of the National Academy of Sciences, USA 98, 14825-14830 (2001) paper at PNAS website (free access) |
