List of Publications

* — corresponding and co-corresponding authors

[45] "Tertiary structural motif sequence statistics enable facile prediction and design of peptides that bind anti-apoptotic Bfl-1 and Mcl-1", V. Frappier, J. M. Jenson, J. Zhou, G. Grigoryan, A. E. Keating, Structure, 27(4): 606-617, 2019 [PubMED] [DOI].

[44] "Tertiary structural motif sequence statistics enable facile prediction and design of peptides that bind anti-apoptotic Bfl-1 and Mcl-1", V. Frappier, J. M. Jenson, J. Zhou, G. Grigoryan, A. E. Keating, bioRxiv, 2018 [DOI].

[43] "A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures", J. Zhou, A. E. Panaitiu, G. Grigoryan, bioRxiv, 2018 [DOI].

[42] "Pareto optimization of combinatorial mutagenesis libraries", D. Verma, G. Grigoryan, C. Bailey-Kellogg, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(4), 2018 [PubMED] [DOI].

[41] "Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials", J. Holland, Q. Pan, G. Grigoryan, PLoS ONE, 13(6): e0199585, 2018 [PubMED] [DOI].

[40] "Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions", L. He, H. Steinocher, A. Shelar, E. B. Cohen, E. N. Heim, B. B. Kragelund, G. Grigoryan, D. DiMaio, eLife, 6: e27701, 2017 [PubMED] [DOI].

[39] "Sequence statistics of tertiary structural motifs reflect protein stability", F. Zheng, G. Grigoryan*, PLoS ONE, 12(5): e0178272, 2017 [PubMED] [DOI].

[38] "Protein Structural Motifs in Prediction and Design", C. O. Mackenzie, G. Grigoryan*, Current Opinion in Structural Biology, 44: 161-167, 2017 [PubMED] [DOI].

[37] "The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases", N. W. Schmidt, G. Grigoryan, W. F. DeGrado, Protein Science, 26(3): 414-435, 2017 [DOI].

[36] "Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport", N. H. Joh, G. Grigoryan, Y. Wu, W. F. DeGrado, Philosophical Transactions B, 372(1726): 20160214, 2017 [PubMED] [DOI].

[35] "Simplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models", F. Zheng, G. Grigoryan*, Methods in Molecular Biology, 1561: 189-200, 2017 [PubMED] [DOI].

[34] "OCoM-SOCoM: Combinatorial mutagenesis library design optimally combining sequence and structure information", D. Verma, G. Grigoryan, C. Bailey-Kellogg, Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 307-316, 2016 [DOI].

[33] "Tertiary Alphabet for the Observable Protein Structural Universe", C. O. Mackenzie, J. Zhou, G. Grigoryan*, Proceedings of the National Academy of Sciences, 113(47): E7438-E7447, 2016 [PubMED] [DOI].


[32] "Graphene Symmetry Amplified by Designed Peptide Self-Assembly", G.-M. Mustata, Y. H. Kim*, J. Zhang, W. F. DeGrado, G. Grigoryan*, M. Wanunu*, Biophysical Journal, 110(11): 2507-2516, 2016 [DOI].


[31] "Protein-Directed Self-Assembly of a Fullerene Crystal", K-H. Kim, D-K. Ko, Y-T. Kim, N. H. Kim, J. Paul, S-Q. Zhang, C. B. Murray, R. Acharya*, W. F. DeGrado*, Y. H. Kim*, G. Grigoryan*, Nature Communications, 7: 11429, 2016 [DOI].


[30] "Design of Specific Peptide-Protein Recognition", F. Zheng, G. Grigoryan*, Methods in Molecular Biology, 1414: 249-263, 2016 [DOI].

[29] "Deletion of Na+/H+ exchanger regulatory factor 2 represses colon cancer progress by suppression of Stat3 and CD24", M. Yoshida, P. He, G. Grigoryan, H. Shim, C. C. Yun, American Journal of Physiology - Gastrointestinal and Liver Physiology, 310(8): G586-G598, 2016 [PubMED] [DOI].

[28] "Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships", F. Zheng, J. Zhang, G. Grigoryan*, Structure, 23(5): 961-971, 2015 [PubMED] [DOI].


[27] "Structure-based design of combinatorial mutagenesis libraries", D. Verma, G. Grigoryan, C. Bailey-Kellogg, Protein Science, 24(5): 895-908, 2015 [DOI].

[26] "Computational Design and Experimental Characterization of Peptides Intended for pH-Dependent Membrane Insertion and Pore Formation", Y. Zhang, R. Bartz, G. Grigoryan, M. Bryant, J. Aaronson, S. Beck, N. Innocent, L. Klein, W. Procopio, T. Tucker, V. Jadhav, D. M. Tellers, William F. DeGrado, ACS Chemical Biology, 10(4): 1082-1093, 2015 [DOI].

[25] "Computational Design of Selective Peptides to Discriminate Between Similar PDZ Domains in an Oncogenic Pathway", F. Zheng, H. Jewell, J. Fitzpatrick, J. Zhang, D. F. Mierke, G. Grigoryan*, Journal of Molecular Biology, 427: 491-510, 2015 [DOI].

[24] "De novo design of a transmembrane Zn2+ transporting four-helix bundle", N. H. Joh, T. Wang, M. P. Bhate, R. Acharya, Y. Wu, M. Grabe*, M. Hong*, G. Grigoryan*, W. F. DeGrado*, Science, 346(6216): 1520-1524, 2014 [DOI].


[23] "Rapid Search for Tertiary Fragments Reveals Protein Sequence-Structure Relationships", J. Zhou, G. Grigoryan*, Protein Science, 24(4): 508-524, 2015 [PubMED] [DOI].

[22] "Design and Designability of Protein-based Assemblies", J. Zhang, F. Zheng, G. Grigoryan*, Current Opinion in Structural Biology, 27: 79-86, 2014 [DOI].

[21] "Absolute Free Energies of Biomolecules from Unperturbed Ensembles", G. Grigoryan*, Journal of Computational Chemistry, 34: 2726–2741, 2013 [PubMED] [DOI].

[20] "Mining Tertiary Structural Motifs for Assessment of Designability", J. Zhang, G. Grigoryan*, Methods in Enzymology, 523: 21-40, 2013 [PubMED] [DOI] [PMC].

[19] "Structural Informatics, Modeling and Design with an Open Source Molecular Software Library (MSL)", D. W. Kulp, S. Subramaniam, J. E. Donald, B. T. Hannigan, B. K. Mueller, G. Grigoryan, A. Senes, Journal of Computational Chemistry, 33(20): 1645-1661, 2012 [PubMED] [DOI].

[18] "Capture and Imaging of a Prehairpin Fusion Intermediate of the Paramyxovirus PIV5", Y. H. Kim, J. E. Donald, G. Grigoryan, G. P. Leser, A. Y. Fadeev , R. A. Lamb, W. F. DeGrado, Proc. Natl. Acad. Sci. USA, 108(52): 20992-20997, 2011 [PubMED] [DOI].

[17] "Computational Design of Virus-like Protein Assemblies on Carbon Nanotube Surfaces", G. Grigoryan, Y. H. Kim, R. Acharya, K. Axelrod, R. M. Jain, L. Willis, M. Drndic, J. M. Kikkawa, and W. F. DeGrado, Science, 332(6033): 1071-1076, 2011 [PubMED] [DOI].

[16] "Transmembrane Communication: General Principles and Lessons from the Structure and Function of the M2 Proton Channel, K+ Channels, and Integrin Receptors", G. Grigoryan, D. T. Moore, and W. F. DeGrado, Annual Review of Biochemistry, 80: 211-237, 2011 [PubMED] [DOI].

[15] "Probing Designability via a Generalized Model of Helical Bundle Geometry", G. Grigoryan* and W. F. DeGrado*, Journal of Molecular Biology, 405(4): 1079-1100, 2011 [PubMED] [DOI].

[14] "Identifying and Reducing Error in Cluster Expansion Approximations of Protein Energies", S. Hahn, O. Ashenberg, G. Grigoryan, and A. E. Keating, Journal of Computational Chemistry, 31(16): 2900-2914, 2010 [PubMED] [DOI].

[13] "Identification of bZIP Interaction Partners of Viral Proteins HBZ, MEQ, BZLF1, and K-bZIP Using Coiled-Coil Arrays", A. W. Reinke, G. Grigoryan, and A. E. Keating, Biochemistry, 49(9): 1985-1997, 2010 [PubMED] [DOI].

[12] "Design of Protein-interaction Specificity Gives Selective bZIP-binding Peptides", G. Grigoryan, A. W. Reinke, and A. E. Keating, Nature, 458: 859-864, 2009 [PubMED] [DOI].

[11] "Cluster-Expansion Models for Flexible-Backbone Protein Energetics", J. R. Apgar, S. Hahn, G. Grigoryan, and A. E. Keating, Journal of Computational Chemistry, 30(15): 2402-2413, 2009 [PubMED] [DOI].

[10] "Structural Specificity in Coiled-coil Interactions", G. Grigoryan and A. E. Keating, Current Opinion in Structural Biology, 18(4): 477-483, 2008 [PubMED] [DOI].

[9] "Modest Membrane Hydrogen Bonds Deliver Rich Results", G. Grigoryan and W. F. DeGrado, Nature Chemical Biology, 4: 393-394, 2008 [PubMED] [DOI].

[8] "Computing van der Waals Energies in the Context of the Rotamer Approximation", G. Grigoryan, A. Ochoa, and A. E. Keating, Proteins: Structure, Function, and Bioinformatics, 68(4): 863-878, 2007 [PubMED] [DOI].

[7] "Ultra-fast Evaluation of Protein Conformational Energies Directly from Sequence", G. Grigoryan, F. Zhou, S. R. Lustig, G. Ceder, D. Morgan and A. E. Keating, PLoS Computational Biology, 2(6): e63, 2006 [PubMED] [DOI].

[6] "Structure-based Prediction of bZIP Partnering Specificity", G. Grigoryan and A. E. Keating, Journal of Molecular Biology, 355(5): 1125-1142, 2006 [PubMED] [DOI].

[5] "Coarse-Graining Protein Energetics in Sequence Variables", F. Zhou, G. Grigoryan, S. R. Lustig, A. E. Keating, G. Ceder, and D. Morgan, Physical Review Letters, 95(14): 148103, 2005 [PubMED] [DOI].

[4] "Design of a Heterospecific, Tetrameric, 21-Residue Miniprotein with Mixed alpha/beta Structure", M. H. Ali, C. M. Taylor, G. Grigoryan, K. N. Allen, B. Imperiali, and A. E. Keating, Structure, 13(2): 225-234, 2005 [PubMED] [DOI].

[3] "Point-based probabilistic surfaces to show surface uncertainty", G. Grigoryan and P. Rheingans, IEEE Transactions On Visualization And Computer Graphics, 10(5): 564-573, 2004 [PubMED] [DOI].

[2] "Probabilistic Surfaces: Point Based Primitives to Show Surface Uncertainty", G. Grigoryan and P. Rheingans, Proceedings of IEEE Visualization, pp. 147-153, 2002 [DOI].

[1] "Using Color to Understand Light Transmission", G. Grigoryan, I.T. Lima, Jr., T. Yu, V.S. Grigoryan, and C.R. Menyuk, Optics and Photonics News, 11(8): 44-50, 2000 [DOI].