Gevorg Grigoryan - Publications

2011- Computer Science Dartmouth University, Hanover, NH, United States 
modeling of protein-peptide interactions

30 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 Zhou J, Panaitiu AE, Grigoryan G. A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 31892539 DOI: 10.1073/pnas.1908723117  0.36
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 Joh NH, Grigoryan G, Wu Y, DeGrado WF. Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 372. PMID 28630154 DOI: 10.1098/rstb.2016.0214  0.96
2016 Schmidt NW, Grigoryan G, DeGrado WF. The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils. Application to understand signaling in histidine kinases. Protein Science : a Publication of the Protein Society. PMID 27977891 DOI: 10.1002/pro.3095  0.96
2016 Mackenzie CO, Zhou J, Grigoryan G. Tertiary alphabet for the observable protein structural universe. Proceedings of the National Academy of Sciences of the United States of America. PMID 27810958 DOI: 10.1073/pnas.1607178113  0.36
2016 Mustata GM, Kim YH, Zhang J, DeGrado WF, Grigoryan G, Wanunu M. Graphene Symmetry Amplified by Designed Peptide Self-Assembly. Biophysical Journal. 110: 2507-2516. PMID 27276268 DOI: 10.1016/j.bpj.2016.04.037  1
2016 Kim KH, Ko DK, Kim YT, Kim NH, Paul J, Zhang SQ, Murray CB, Acharya R, DeGrado WF, Kim YH, Grigoryan G. Protein-directed self-assembly of a fullerene crystal. Nature Communications. 7: 11429. PMID 27113637 DOI: 10.1038/ncomms11429  1
2016 Zheng F, Grigoryan G. Design of Specific Peptide-Protein Recognition. Methods in Molecular Biology (Clifton, N.J.). 1414: 249-63. PMID 27094296 DOI: 10.1007/978-1-4939-3569-7_15  1
2016 Yoshida M, Zhao L, Grigoryan G, Shim H, He P, Yun CC. Deletion of Na+/H+ exchanger regulatory factor 2 represses colon cancer progress by suppression of Stat3 and CD24. American Journal of Physiology. Gastrointestinal and Liver Physiology. ajpgi.00419.2015. PMID 26867566 DOI: 10.1152/ajpgi.00419.2015  1
2015 Zhang Y, Bartz R, Grigoryan G, Bryant M, Aaronson J, Beck S, Innocent N, Klein L, Procopio W, Tucker T, Jadhav V, Tellers DM, DeGrado WF. Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation. Acs Chemical Biology. 10: 1082-93. PMID 25630033 DOI: 10.1021/cb500759p  1
2015 Verma D, Grigoryan G, Bailey-Kellogg C. Structure-based design of combinatorial mutagenesis libraries. Protein Science : a Publication of the Protein Society. 24: 895-908. PMID 25611189 DOI: 10.1002/pro.2642  1
2015 Zheng F, Jewell H, Fitzpatrick J, Zhang J, Mierke DF, Grigoryan G. Computational design of selective peptides to discriminate between similar PDZ domains in an oncogenic pathway. Journal of Molecular Biology. 427: 491-510. PMID 25451599 DOI: 10.1016/j.jmb.2014.10.014  1
2015 Zhou J, Grigoryan G. Rapid search for tertiary fragments reveals protein sequence-structure relationships. Protein Science : a Publication of the Protein Society. 24: 508-24. PMID 25420575 DOI: 10.1002/pro.2610  0.36
2014 Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. De novo design of a transmembrane Zn²⁺-transporting four-helix bundle. Science (New York, N.Y.). 346: 1520-4. PMID 25525248 DOI: 10.1126/science.1261172  1
2012 Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). Journal of Computational Chemistry. 33: 1645-61. PMID 22565567 DOI: 10.1002/jcc.22968  1
2011 Kim YH, Donald JE, Grigoryan G, Leser GP, Fadeev AY, Lamb RA, DeGrado WF. Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5. Proceedings of the National Academy of Sciences of the United States of America. 108: 20992-7. PMID 22178759 DOI: 10.1073/pnas.1116034108  1
2011 Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science (New York, N.Y.). 332: 1071-6. PMID 21617073 DOI: 10.1126/science.1198841  1
2011 Grigoryan G, Moore DT, DeGrado WF. Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors. Annual Review of Biochemistry. 80: 211-37. PMID 21548783 DOI: 10.1146/annurev-biochem-091008-152423  1
2011 Grigoryan G, Degrado WF. Probing designability via a generalized model of helical bundle geometry. Journal of Molecular Biology. 405: 1079-100. PMID 20932976 DOI: 10.1016/j.jmb.2010.08.058  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, 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
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 Grigoryan G, Degrado WF. Modest membrane hydrogen bonds deliver rich results. Nature Chemical Biology. 4: 393-4. PMID 18560430 DOI: 10.1038/nchembio0708-393  1
2008 Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions Current Opinion in Structural Biology. 18: 477-483. PMID 18555680 DOI: 10.1016/  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
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
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 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
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