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Apgar JR, Hahn S, Grigoryan G, Keating AE.  2009.  Cluster expansion models for flexible-backbone protein energetics.. Journal of computational chemistry. 30:2402–13.
Zhou F, Grigoryan G, Lustig SR, Keating AE, Ceder G, Morgan D.  2005.  Coarse-graining protein energetics in sequence variables.. Physical review letters. 95:148103.
Keating AE, Shin SH, Houk K.N, Garcia-Garibay MA.  1997.  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.
Newman JRS, Keating AE.  2003.  Comprehensive identification of human bZIP interactions with coiled-coil arrays.. Science (New York, N.Y.). 300:2097–101.
Garcia-Garibay MA, Houk K.N, Keating AE, Cheer CJ, Leibovitch M, Scheffer JR, Wu L-C.  1999.  Computational Prediction of the Enantioselectivity of a Solid-State Photoreaction. Organic Letters. 1:1279–1281.
Zhang H, Chen J, Wang Y, Peng L, Dong X, Lu Y, Keating AE, Jiang T.  2009.  A computationally guided protein-interaction screen uncovers coiled-coil interactions involved in vesicular trafficking.. Journal of molecular biology. 392:228–41.
Grigoryan G, Ochoa A, Keating AE.  2007.  Computing van der Waals energies in the context of the rotamer approximation.. Proteins. 68:863–78.
Shin SH, Cizmeciyan D, Keating AE, Khan SI, Garcia-Garibay MA.  1997.  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.
Potapov V, Kaplan JB, Keating AE.  2015.  Data-driven prediction and design of bZIP coiled-coil interactions.. PLoS Comput Biol. 11(2):e1004046.
Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE.  2005.  Design of a Heterospecific, Tetrameric, 21-Residue Miniprotein with Mixed $\alpha$/$\beta$ Structure. Structure. 13:225–234.
T Chen S, Reinke AW, Keating AE.  2011.  Design of peptide inhibitors that bind the bZIP domain of Epstein-Barr virus protein BZLF1.. Journal of molecular biology. 408:304–20.
Grigoryan G, Reinke AW, Keating AE.  2009.  Design of protein-interaction specificity gives selective bZIP-binding peptides.. Nature. 458:859–64.
Foight GWink, Ryan JA, Gullá SV, Letai A, Keating AE.  2014.  Designed BH3 peptides with high affinity and specificity for targeting Mcl-1 in cells.. ACS Chem Biol. 9(9):1962-8.
T. Chen S, Keating AE.  2012.  Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods. Protein Science. 21:949–963.
Dutta S, Gullá S, T Chen S, Fire E, Grant RA, Keating AE.  2010.  Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL.. Journal of molecular biology. 398:747–62.
Ashenberg O, Rozen-Gagnon K, Laub MT, Keating AE.  2011.  Determinants of homodimerization specificity in histidine kinases.. Journal of molecular biology. 413:222–35.