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Amy E. Keating - Publications

Affiliations: 
Biology Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
Computational, biophysical, structural and proteomic studies of protein-protein interactions
Website:
https://biology.mit.edu/people/amy_keating
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90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Frappier V, Jenson JM, Zhou J, Grigoryan G, Keating AE. Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1. Structure (London, England : 1993). PMID 30773399 DOI: 10.1016/j.str.2019.01.008  1
2017 Foight GW, Chen TS, Richman D, Keating AE. Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design. Methods in Molecular Biology (Clifton, N.J.). 1561: 213-232. PMID 28236241 DOI: 10.1007/978-1-4939-6798-8_13  0.36
2017 Rodriguez-Martinez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ. Combinatorial bZIP dimers define complex DNA-binding specificity landscapes. Elife. 6. PMID 28186491 DOI: 10.7554/eLife.19272  0.72
2016 Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Current Opinion in Structural Biology. 39: 27-38. PMID 27123812 DOI: 10.1016/j.sbi.2016.04.001  1
2016 Rezaei Araghi R, Ryan JA, Letai A, Keating AE. Rapid Optimization of Mcl-1 Inhibitors using Stapled Peptide Libraries Including Non-Natural Side Chains. Acs Chemical Biology. PMID 26854535 DOI: 10.1021/acschembio.5b01002  1
2016 Chang JB, Kim YH, Thompson E, No YH, Kim NH, Arrieta J, Manfrinato VR, Keating AE, Berggren KK. The Orientations of Large Aspect-Ratio Coiled-Coil Proteins Attached to Gold Nanostructures. Small (Weinheim An Der Bergstrasse, Germany). PMID 26799936 DOI: 10.1002/smll.201502419  1
2016 Foight GW, Keating AE. Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5. Protein Science : a Publication of the Protein Society. PMID 26779844 DOI: 10.1002/pro.2881  1
2015 Sirin S, Apgar JR, Bennett EM, Keating AE. AB-Bind: Antibody binding mutational database for computational affinity predictions. Protein Science : a Publication of the Protein Society. PMID 26473627 DOI: 10.1002/pro.2829  0.8
2015 Potapov V, Kaplan JB, Keating AE. Data-driven prediction and design of bZIP coiled-coil interactions. Plos Computational Biology. 11: e1004046. PMID 25695764 DOI: 10.1371/journal.pcbi.1004046  1
2015 Potapov V, Kaplan JB, Keating AE. Data-driven prediction and design of bZIP coiled-coil interactions. Plos Computational Biology. 11: e1004046. PMID 25695764 DOI: 10.1371/journal.pcbi.1004046  1
2015 Dutta S, Ryan J, Chen TS, Kougentakis C, Letai A, Keating AE. Potent and specific peptide inhibitors of human pro-survival protein Bcl-xL. Journal of Molecular Biology. 427: 1241-53. PMID 25451027 DOI: 10.1016/j.jmb.2014.09.030  1
2015 Dutta S, Ryan J, Chen TS, Kougentakis C, Letai A, Keating AE. Potent and specific peptide inhibitors of human pro-survival protein Bcl-xL. Journal of Molecular Biology. 427: 1241-53. PMID 25451027 DOI: 10.1016/j.jmb.2014.09.030  1
2015 Foight GW, Keating AE. Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins Journal of Molecular Biology. 427: 2468-2490. DOI: 10.1016/j.jmb.2015.05.015  1
2015 Reich L, Dutta S, Keating AE. SORTCERY - A High-Throughput Method to Affinity Rank Peptide Ligands Journal of Molecular Biology. 427: 2135-2150. DOI: 10.1016/j.jmb.2014.09.025  1
2014 Foight GW, Ryan JA, Gullá SV, Letai A, Keating AE. Designed BH3 peptides with high affinity and specificity for targeting Mcl-1 in cells. Acs Chemical Biology. 9: 1962-8. PMID 25052212 DOI: 10.1021/cb500340w  1
2014 Foight GW, Ryan JA, Gullá SV, Letai A, Keating AE. Designed BH3 peptides with high affinity and specificity for targeting Mcl-1 in cells. Acs Chemical Biology. 9: 1962-8. PMID 25052212 DOI: 10.1021/cb500340w  1
2014 Kaplan JB, Reinke AW, Keating AE. Increasing the affinity of selective bZIP-binding peptides through surface residue redesign. Protein Science : a Publication of the Protein Society. 23: 940-53. PMID 24729132 DOI: 10.1002/pro.2477  1
2014 Kaplan JB, Reinke AW, Keating AE. Increasing the affinity of selective bZIP-binding peptides through surface residue redesign. Protein Science : a Publication of the Protein Society. 23: 940-53. PMID 24729132 DOI: 10.1002/pro.2477  1
2014 DeBartolo J, Taipale M, Keating AE. Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins Plos Computational Biology. 10. DOI: 10.1371/journal.pcbi.1003693  1
2014 Negron C, Keating AE. A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit Journal of the American Chemical Society. 136: 16544-16556. DOI: 10.1021/ja507847t  1
2013 Reinke AW, Baek J, Ashenberg O, Keating AE. Networks of bZIP protein-protein interactions diversified over a billion years of evolution. Science (New York, N.Y.). 340: 730-4. PMID 23661758 DOI: 10.1126/science.1233465  0.92
2013 Keating AE. Methods in Enzymology. Methods in protein design. Preface. Methods in Enzymology. 523: xvii-xviii. PMID 23422442  1
2013 Negron C, Keating AE. Multistate protein design using CLEVER and CLASSY Methods in Enzymology. 523: 171-190. PMID 23422430 DOI: 10.1016/B978-0-12-394292-0.00008-4  1
2013 Dutta S, Chen TS, Keating AE. Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening Acs Chemical Biology. 8: 778-788. PMID 23363053 DOI: 10.1021/cb300679a  1
2013 Ashenberg O, Keating AE, Laub MT. Helix bundle loops determine whether histidine kinases autophosphorylate in cis or in trans Journal of Molecular Biology. 425: 1198-1209. PMID 23333741 DOI: 10.1016/j.jmb.2013.01.011  1
2013 Yin WB, Reinke AW, Szilágyi M, Emri T, Chiang YM, Keating AE, Pócsi I, Wang CC, Keller NP. bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans. Microbiology (Reading, England). 159: 77-88. PMID 23154967 DOI: 10.1099/mic.0.063370-0  1
2013 Yin WB, Reinke AW, Szilágyi M, Emri T, Chiang YM, Keating AE, Pócsi I, Wang CC, Keller NP. bZIP transcription factors affecting secondary metabolism, sexual development and stress responses in Aspergillus nidulans. Microbiology (Reading, England). 159: 77-88. PMID 23154967 DOI: 10.1099/mic.0.063370-0  1
2013 Chen TS, Palacios H, Keating AE. Structure-based redesign of the binding specificity of anti-apoptotic Bcl-xL Journal of Molecular Biology. 425: 171-185. PMID 23154169 DOI: 10.1016/j.jmb.2012.11.009  1
2013 Reinke AW, Baek J, Ashenberg O, Keating AE. Networks of bZIP protein-protein interactions diversified over a billion years of evolution Science. 340: 730-734. DOI: 10.1126/science.1233465  1
2013 Reinke AW, Baek J, Ashenberg O, Keating AE. Networks of bZIP protein-protein interactions diversified over a billion years of evolution Science. 340: 730-734. DOI: 10.1126/science.1233465  0.92
2012 London N, Gullá S, Keating AE, Schueler-Furman O. In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. Biochemistry. 51: 5841-50. PMID 22702834 DOI: 10.1021/bi3003567  1
2012 London N, Gullá S, Keating AE, Schueler-Furman O. In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. Biochemistry. 51: 5841-50. PMID 22702834 DOI: 10.1021/bi3003567  1
2012 Debartolo J, Dutta S, Reich L, Keating AE. Predictive Bcl-2 family binding models rooted in experiment or structure Journal of Molecular Biology. 422: 124-144. PMID 22617328 DOI: 10.1016/j.jmb.2012.05.022  1
2012 Chen TS, Keating AE. Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods Protein Science. 21: 949-963. PMID 22593041 DOI: 10.1002/pro.2096  1
2012 Thompson KE, Bashor CJ, Lim WA, Keating AE. Synzip protein interaction toolbox: In vitro and in vivo specifications of heterospecific coiled-coil interaction domains Acs Synthetic Biology. 1: 118-129. PMID 22558529 DOI: 10.1021/sb200015u  1
2011 Trigg J, Gutwin K, Keating AE, Berger B. Multicoil2: Predicting coiled coils and their oligomerization states from sequence in the twilight zone Plos One. 6. PMID 21901122 DOI: 10.1371/journal.pone.0023519  1
2011 Ashenberg O, Rozen-Gagnon K, Laub MT, Keating AE. Determinants of homodimerization specificity in histidine kinases Journal of Molecular Biology. 413: 222-235. PMID 21854787 DOI: 10.1016/j.jmb.2011.08.011  1
2011 Chen TS, Reinke AW, Keating AE. Design of peptide inhibitors that bind the bZIP domain of Epstein-Barr virus protein BZLF1 Journal of Molecular Biology. 408: 304-320. PMID 21354428 DOI: 10.1016/j.jmb.2011.02.046  1
2011 Schreiber G, Keating AE. Protein binding specificity versus promiscuity Current Opinion in Structural Biology. 21: 50-61. PMID 21071205 DOI: 10.1016/j.sbi.2010.10.002  1
2010 Hahn S, Ashenberg O, Grigoryan G, Keating AE. Identifying and reducing error in cluster-expansion approximations of protein energies Journal of Computational Chemistry. 31: 2900-2914. PMID 20602445 DOI: 10.1002/jcc.21585  1
2010 Reinke AW, Grant RA, Keating AE. A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering Journal of the American Chemical Society. 132: 6025-6031. PMID 20387835 DOI: 10.1021/ja907617a  1
2010 Dutta S, Gullá S, Chen TS, Fire E, Grant RA, Keating AE. Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-xL Journal of Molecular Biology. 398: 747-762. PMID 20363230 DOI: 10.1016/j.jmb.2010.03.058  1
2010 Zizlsperger N, Keating AE. Specific coiled-coil interactions contribute to a global model of the structure of the spindle pole body Journal of Structural Biology. 170: 246-256. PMID 20139001 DOI: 10.1016/j.jsb.2010.01.022  1
2010 Reinke AW, Grigoryan G, Keating AE. Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays Biochemistry. 49: 1985-1997. PMID 20102225 DOI: 10.1021/bi902065k  1
2010 Fire E, Gullá SV, Grant RA, Keating AE. Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes Protein Science. 19: 507-519. PMID 20066663 DOI: 10.1002/pro.329  1
2010 Stewart ML, Fire E, Keating AE, Walensky LD. The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer Nature Chemical Biology. 6: 595-601. DOI: 10.1038/nchembio.391  1
2009 Zhang H, Chen J, Wang Y, Peng L, Dong X, Lu Y, Keating AE, Jiang T. A Computationally Guided Protein-Interaction Screen Uncovers Coiled-Coil Interactions Involved in Vesicular Trafficking Journal of Molecular Biology. 392: 228-241. PMID 19591838 DOI: 10.1016/j.jmb.2009.07.006  1
2009 Schneider M, Fu X, Keating AE. X-ray vs. NMR structures as templates for computational protein design Proteins: Structure, Function and Bioinformatics. 77: 97-110. PMID 19422060 DOI: 10.1002/prot.22421  1
2009 Grigoryan G, Reinke AW, Keating AE. Design of protein-interaction specificity gives selective bZIP-binding peptides Nature. 458: 859-864. PMID 19370028 DOI: 10.1038/nature07885  1
2009 Apgar JR, Seungsoo H, Grigoryan G, Keating AE. Cluster expansion models for flexible-backbone protein energetics Journal of Computational Chemistry. 30: 2402-2413. PMID 19360809 DOI: 10.1002/jcc.21249  1
2008 Zizlsperger N, Malashkevich VN, Pillay S, Keating AE. Analysis of coiled-coil interactions between core proteins of the spindle pole body Biochemistry. 47: 11858-11868. PMID 18850724 DOI: 10.1021/bi801378z  1
2008 Zizlsperger N, Malashkevich VN, Pillay S, Keating AE. Analysis of coiled-coil interactions between core proteins of the spindle pole body Biochemistry. 47: 11858-11868. PMID 18850724 DOI: 10.1021/bi801378z  0.6
2008 Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions Current Opinion in Structural Biology. 18: 477-483. PMID 18555680 DOI: 10.1016/j.sbi.2008.04.008  1
2008 Apgar JR, Gutwin KN, Keating AE. Predicting helix orientation for coiled-coil dimers Proteins: Structure, Function and Genetics. 72: 1048-1065. PMID 18506779 DOI: 10.1002/prot.22118  1
2007 Fu X, Apgar JR, Keating AE. Modeling Backbone Flexibility to Achieve Sequence Diversity: The Design of Novel α-Helical Ligands for Bcl-xL Journal of Molecular Biology. 371: 1099-1117. PMID 17597151 DOI: 10.1016/j.jmb.2007.04.069  1
2007 Grigoryan G, Ochoa A, Keating AE. Computing van der Waals energies in the context of the rotamer approximation Proteins: Structure, Function and Genetics. 68: 863-878. PMID 17554777 DOI: 10.1002/prot.21470  1
2007 Keating AE. A rational route to probing membrane proteins Genome Biology. 8. PMID 17540048 DOI: 10.1186/gb-2007-8-5-214  1
2006 Grigoryan G, Zhou F, Lustig SR, Ceder G, Morgan D, Keating AE. Ultra-fast evaluation of protein energies directly from sequence Plos Computational Biology. 2: 0551-0563. PMID 16789811 DOI: 10.1371/journal.pcbi.0020063  1
2006 Grigoryan G, Keating AE. Structure-based prediction of bZIP partnering specificity Journal of Molecular Biology. 355: 1125-1142. PMID 16359704 DOI: 10.1016/j.jmb.2005.11.036  1
2006 McDonnell AV, Jiang T, Keating AE, Berger B. Paircoil2: Improved prediction of coiled coils from sequence Bioinformatics. 22: 356-358. PMID 16317077 DOI: 10.1093/bioinformatics/bti797  1
2005 Taylor CM, Keating AE. Orientation and oligomerization specificity of the Bcr coiled-coil oligomerization domain Biochemistry. 44: 16246-16256. PMID 16331985 DOI: 10.1021/bi051493t  1
2005 Zhou F, Grigoryan G, Lustig SR, Keating AE, Ceder G, Morgan D. Coarse-graining protein energetics in sequence variables Physical Review Letters. 95. PMID 16241695 DOI: 10.1103/PhysRevLett.95.148103  1
2005 Jiang T, Keating AE. AVID: An integrative framework for discovering functional relationship among proteins Bmc Bioinformatics. 6. PMID 15929793 DOI: 10.1186/1471-2105-6-136  1
2005 Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure (London, England : 1993). 13: 225-34. PMID 15698566 DOI: 10.1016/j.str.2004.12.009  1
2005 Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure (London, England : 1993). 13: 225-34. PMID 15698566 DOI: 10.1016/j.str.2004.12.009  1
2004 Fong JH, Keating AE, Singh M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biology. 5: R11. PMID 14759261  1
2003 Newman JRS, Keating AE. Comprehensive identification of human bZIP interactions with coiled-coil arrays Science. 300: 2097-2101. PMID 12805554 DOI: 10.1126/science.1084648  1
2002 Keating TA, Marshall CG, Walsh CT, Keating AE. The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains Nature Structural Biology. 9: 522-526. PMID 12055621 DOI: 10.1038/nsb810  1
2001 Keating AE, Malashkevich VN, Tidor B, Kim PS. Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Proceedings of the National Academy of Sciences of the United States of America. 98: 14825-30. PMID 11752430 DOI: 10.1073/pnas.261563398  1
2001 Keating AE, Malashkevich VN, Tidor B, Kim PS. Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Proceedings of the National Academy of Sciences of the United States of America. 98: 14825-30. PMID 11752430 DOI: 10.1073/pnas.261563398  1
1999 Keating AE, Merrigan SR, Singleton DA, Houk KN. Experimental proof of the non-least-motion cycloadditions of dichlorocarbene to alkenes: Kinetic isotope effects and quantum mechanical transition states Journal of the American Chemical Society. 121: 3933-3938. DOI: 10.1021/ja981427x  0.56
1999 Keating AE, Merrigan SR, Singleton DA, Houk KN. Experimental proof of the non-least-motion cycloadditions of dichlorocarbene to alkenes: Kinetic isotope effects and quantum mechanical transition states Journal of the American Chemical Society. 121: 3933-3938. DOI: 10.1021/ja981427x  0.56
1999 Keating AE, Shin SH, Huang FK, Garrell RL, Garcia-Garibay MA. Experimental and computational modeling of biphenyl twisting in a solid- to-solid carbene reaction Tetrahedron Letters. 40: 261-264. DOI: 10.1016/S0040-4039(98)02351-X  0.56
1999 Keating AE, Shin SH, Huang FK, Garrell RL, Garcia-Garibay MA. Experimental and computational modeling of biphenyl twisting in a solid- to-solid carbene reaction Tetrahedron Letters. 40: 261-264. DOI: 10.1016/S0040-4039(98)02351-X  0.56
1999 Garcia-Garibay MA, Houk KN, Keating AE, Cheer CJ, Leibovitch M, Scheffer JR, Wu LC. Computational prediction of the enantioselectivity of a solid-state photoreaction Organic Letters. 1: 1279-1281.  0.56
1999 Garcia-Garibay MA, Houk KN, Keating AE, Cheer CJ, Leibovitch M, Scheffer JR, Wu LC. Computational prediction of the enantioselectivity of a solid-state photoreaction Organic Letters. 1: 1279-1281.  0.56
1998 Keating AE, Garcia-Garibay MA, Houk KN. Influence of bystander substituents on the rates of 1,2-H and 1,2-Ph shifts in singlet and triplet carbenes Journal of Physical Chemistry A. 102: 8467-8476.  0.56
1998 Keating AE, Garcia-Garibay MA, Houk KN. Influence of bystander substituents on the rates of 1,2-H and 1,2-Ph shifts in singlet and triplet carbenes Journal of Physical Chemistry A. 102: 8467-8476.  0.68
1997 Keating AE, Garcia-Garibay MA, Houk KN. Origins of stereoselective carbene 1,2-shifts and cycloadditions of 1,2-dichloroethylidene: A theoretical model based on CBS-Q and B3LYP calculations Journal of the American Chemical Society. 119: 10805-10809. DOI: 10.1021/ja970642v  0.56
1997 Keating AE, Garcia-Garibay MA, Houk KN. Origins of stereoselective carbene 1,2-shifts and cycloadditions of 1,2-dichloroethylidene: A theoretical model based on CBS-Q and B3LYP calculations Journal of the American Chemical Society. 119: 10805-10809. DOI: 10.1021/ja970642v  0.68
1997 Shin SH, Cizmeciyan D, Keating AE, Khan SI, Garcia-Garibay MA. Control of carbene reactivity by crystals. A highly selective 1,2-H shift in the solid-to-solid reaction of 1-(4'-biphenylyl)-2-phenyldiazopropane to (Z)-1-(4'-biphenylyl)-2-phenylpropene Journal of the American Chemical Society. 119: 1859-1868. DOI: 10.1021/ja9633225  0.56
1997 Shin SH, Cizmeciyan D, Keating AE, Khan SI, Garcia-Garibay MA. Control of carbene reactivity by crystals. A highly selective 1,2-H shift in the solid-to-solid reaction of 1-(4'-biphenylyl)-2-phenyldiazopropane to (Z)-1-(4'-biphenylyl)-2-phenylpropene Journal of the American Chemical Society. 119: 1859-1868. DOI: 10.1021/ja9633225  0.68
1997 Keating AE, Shin SH, Houk KN, Garcia-Garibay MA. Combining quantum mechanical reaction pathways with force field lattice interactions to model a solid-state phototransformation Journal of the American Chemical Society. 119: 1474-1475. DOI: 10.1021/ja962734a  0.56
1997 Keating AE, Shin SH, Houk KN, Garcia-Garibay MA. Combining quantum mechanical reaction pathways with force field lattice interactions to model a solid-state phototransformation Journal of the American Chemical Society. 119: 1474-1475. DOI: 10.1021/ja962734a  0.68
1997 Nakamura K, Sheu C, Keating AE, Houk KN, Sherman JC, Chapman RG, Jorgensen WL. Self-assembling ternary complex stabilities and template ratios in carceplex formation Journal of the American Chemical Society. 119: 4321-4322. DOI: 10.1021/ja9623065  0.56
1997 Nakamura K, Sheu C, Keating AE, Houk KN, Sherman JC, Chapman RG, Jorgensen WL. Self-assembling ternary complex stabilities and template ratios in carceplex formation Journal of the American Chemical Society. 119: 4321-4322. DOI: 10.1021/ja9623065  0.56
1996 Houk KN, Nakamura K, Sheu C, Keating AE. Gating as a control element in constrictive binding and guest release by hemicarcerands. Science (New York, N.Y.). 273: 627-9. PMID 8662548 DOI: 10.1126/science.273.5275.627  0.56
1996 Houk KN, Nakamura K, Sheu C, Keating AE. Gating as a control element in constrictive binding and guest release by hemicarcerands. Science (New York, N.Y.). 273: 627-9. PMID 8662548 DOI: 10.1126/science.273.5275.627  0.56
1996 Shin SH, Keating AE, Garcia-Giarbay MA. Transforming a nonselective carberne rearrangement into a highly selective process by using crystalline media Journal of the American Chemical Society. 118: 7626-7627. DOI: 10.1021/ja9533398  0.56
1996 Shin SH, Keating AE, Garcia-Giarbay MA. Transforming a nonselective carberne rearrangement into a highly selective process by using crystalline media Journal of the American Chemical Society. 118: 7626-7627. DOI: 10.1021/ja9533398  0.52
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