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Gevorg Grigoryan - Publications

Affiliations: 
2011- Computer Science Dartmouth University, Hanover, NH, United States 
Area:
modeling of protein-peptide interactions
Website:
https://home.dartmouth.edu/faculty-directory/gevorg-grigoryan
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51 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
2023 Ingraham JB, Baranov M, Costello Z, Barber KW, Wang W, Ismail A, Frappier V, Lord DM, Ng-Thow-Hing C, Van Vlack ER, Tie S, Xue V, Cowles SC, Leung A, Rodrigues JV, ... ... Grigoryan G, et al. Illuminating protein space with a programmable generative model. Nature. PMID 37968394 DOI: 10.1038/s41586-023-06728-8  0.378
2022 Li AJ, Lu M, Desta I, Sundar V, Grigoryan G, Keating AE. Neural Network-Derived Potts Models for Structure-Based Protein Design using Backbone Atomic Coordinates and Tertiary Motifs. Protein Science : a Publication of the Protein Society. e4554. PMID 36564857 DOI: 10.1002/pro.4554  0.665
2022 Swanson S, Sivaraman V, Grigoryan G, Keating AE. Tertiary motifs as building blocks for the design of protein-binding peptides. Protein Science : a Publication of the Protein Society. 31: e4322. PMID 35634780 DOI: 10.1002/pro.4322  0.614
2022 Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, ... ... Grigoryan G, et al. Large-scale design and refinement of stable proteins using sequence-only models. Plos One. 17: e0265020. PMID 35286324 DOI: 10.1371/journal.pone.0265020  0.386
2022 Holland J, Grigoryan G. Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences. Protein Science : a Publication of the Protein Society. 31: 900-917. PMID 35060221 DOI: 10.1002/pro.4280  0.365
2021 Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nature Communications. 12: 407. PMID 33462223 DOI: 10.1038/s41467-020-20689-w  0.375
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  0.537
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  0.697
2018 Verma D, Grigoryan G, Bailey-Kellogg C. Pareto optimization of combinatorial mutagenesis libraries. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30040654 DOI: 10.1109/Tcbb.2018.2858794  0.415
2018 Holland J, Pan Q, Grigoryan G. Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials. Plos One. 13: e0199585. PMID 29953468 DOI: 10.1371/Journal.Pone.0199585  0.34
2017 He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions. Elife. 6. PMID 28869036 DOI: 10.7554/Elife.27701  0.371
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  0.537
2017 Zheng F, Grigoryan G. Sequence statistics of tertiary structural motifs reflect protein stability. Plos One. 12: e0178272. PMID 28552940 DOI: 10.1371/Journal.Pone.0178272  0.48
2017 Mackenzie CO, Grigoryan G. Protein structural motifs in prediction and design. Current Opinion in Structural Biology. 44: 161-167. PMID 28460216 DOI: 10.1016/J.Sbi.2017.03.012  0.496
2017 Zheng F, Grigoryan G. Simplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models. Methods in Molecular Biology (Clifton, N.J.). 1561: 189-200. PMID 28236239 DOI: 10.1007/978-1-4939-6798-8_11  0.53
2017 He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Author response: Single methyl groups can act as toggle switches to specify transmembrane Protein-protein interactions Elife. DOI: 10.7554/Elife.27701.021  0.323
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  0.569
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  0.459
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  0.516
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  0.674
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  0.454
2015 Zheng F, Zhang J, Grigoryan G. Tertiary structural propensities reveal fundamental sequence/structure relationships. Structure (London, England : 1993). 23: 961-71. PMID 25914055 DOI: 10.1016/J.Str.2015.03.015  0.466
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  0.534
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  0.517
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  0.452
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  0.521
2015 Sapkota B, Mustata M, Zhang J, Grigoryan G, Wanunu M. DNA-Binding Properties of Peptide-Functionalized Graphene Quantum Dots Biophysical Journal. 108: 393a. DOI: 10.1016/J.Bpj.2014.11.2153  0.304
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  0.543
2014 Zhang J, Zheng F, Grigoryan G. Design and designability of protein-based assemblies. Current Opinion in Structural Biology. 27: 79-86. PMID 24952313 DOI: 10.1016/J.Sbi.2014.05.009  0.475
2013 Grigoryan G. Absolute free energies of biomolecules from unperturbed ensembles. Journal of Computational Chemistry. 34: 2726-41. PMID 24132787 DOI: 10.1002/Jcc.23448  0.442
2013 Zhang J, Grigoryan G. Mining tertiary structural motifs for assessment of designability. Methods in Enzymology. 523: 21-40. PMID 23422424 DOI: 10.1016/B978-0-12-394292-0.00002-3  0.512
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  0.693
2012 Grigoryan G. Making Picky Proteins: Computational Design of Interaction Specificity Biophysical Journal. 102: 438a-439a. DOI: 10.1016/J.Bpj.2011.11.2401  0.491
2012 Joh NH, Grigoryan G, Hu Y, DeGrado WF. Testing the Structural Mechanism of Transmembrane Translocation using De-Novo Designed Soft-Metal Transporters with Inverted Dual Topology Biophysical Journal. 102: 231a. DOI: 10.1016/J.Bpj.2011.11.1269  0.535
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  0.533
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  0.539
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  0.447
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  0.614
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  0.736
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  0.591
2010 Grigoryan G. Md-Based Method for Computing Configuration Integrals Provides Ability to Test Force Fields Biophysical Journal. 98: 567a. DOI: 10.1016/J.Bpj.2009.12.3076  0.393
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  0.677
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  0.704
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  0.454
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  0.664
2008 Span LM, Grigoryan G, Bennett JS, DeGrado WF. Factors That Influence the Homo- and Hetero-Oligomerization of the Leukocyte Integrin Transmembrane Domains Blood. 112: 3556-3556. DOI: 10.1182/Blood.V112.11.3556.3556  0.505
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  0.683
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  0.689
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  0.668
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  0.659
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  0.74
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