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Garegin A. (Garyk) Papoian - Publications

Affiliations: 
2004-2010 University of North Carolina, Chapel Hill, Chapel Hill, NC 
 2010- Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
computational methods, to study biological processes
Website:
http://www.chem.umd.edu/faculty-staff-directory/facultydirectory/garegin-papoian
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60 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
2024 Zhao H, Wu H, Guseman A, Abeykoon D, Camara CM, Dalal Y, Fushman D, Papoian GA. The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. Plos Computational Biology. 20: e1011721. PMID 38181064 DOI: 10.1371/journal.pcbi.1011721  0.778
2021 Wu H, Dalal Y, Papoian GA. Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle. Journal of Molecular Biology. 166881. PMID 33617899 DOI: 10.1016/j.jmb.2021.166881  0.649
2020 Jin S, Contessoto VG, Chen M, Schafer NP, Lu W, Chen X, Bueno C, Hajitaheri A, Sirovetz BJ, Davtyan A, Papoian GA, Tsai MY, Wolynes PG. AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Research. PMID 32383764 DOI: 10.1093/Nar/Gkaa356  0.754
2020 Pitman M, Dalal Y, Papoian GA. Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes. Biophysical Journal. PMID 32097625 DOI: 10.1016/J.Bpj.2020.01.042  0.657
2020 Pitman M, Dalal Y, Papoian GA, Melters DP, Rakshit T, Dimitriadis EK, Bui M. Computational Modeling of Nucleosomal Mechanics and Epigenetic Modifications Biophysical Journal. 118: 9a. DOI: 10.1016/J.Bpj.2019.11.3372  0.61
2020 Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. A Balance Between Elastic and Rigidified CENP-A Nucleosomes Govern Centromeric Chromatin Fidelity Biophysical Journal. 118: 8a. DOI: 10.1016/J.Bpj.2019.11.3369  0.609
2019 Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners. Proceedings of the National Academy of Sciences of the United States of America. PMID 31712435 DOI: 10.1073/Pnas.1911880116  0.644
2019 Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophysical Journal. PMID 31005236 DOI: 10.1016/J.Bpj.2019.03.021  0.777
2019 Wu H, Dalal Y, Papoian GA. Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle Biophysical Journal. 116: 70a. DOI: 10.1016/J.Bpj.2018.11.421  0.624
2019 Pitman M, Dalal Y, Papoian GA. Cenp-A Hijacks the Histone Chaperone Network in Cancer--Computational Insights Biophysical Journal. 116: 436a. DOI: 10.1016/J.Bpj.2018.11.2347  0.587
2018 Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 30091924 DOI: 10.1021/Acs.Jpcb.8B05791  0.499
2017 Bui M, Pitman M, Nuccio A, Roque S, Donlin-Asp PG, Nita-Lazar A, Papoian GA, Dalal Y. Internal modifications in the CENP-A nucleosome modulate centromeric dynamics. Epigenetics & Chromatin. 10: 17. PMID 28396698 DOI: 10.1186/S13072-017-0124-6  0.637
2016 Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian GA. Promiscuous histone mis-assembly is actively prevented by chaperones. Journal of the American Chemical Society. PMID 27454815 DOI: 10.1021/Jacs.6B05355  0.757
2016 Zhang B, Zheng W, Papoian GA, Wolynes PG. Exploring the Free Energy Landscape of Nucleosomes. Journal of the American Chemical Society. PMID 27300314 DOI: 10.1021/Jacs.6B02893  0.592
2016 Davtyan A, Platkov M, Gruebele M, Papoian GA. Stochastic Resonance in Protein Folding Dynamics. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 26992148 DOI: 10.1002/Cphc.201501125  0.636
2015 Gruebele M, Dave K, Davtyan A, Papoian GA, Platkov M. Environmental fluctuations and stochastic resonance in protein folding. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 26711088 DOI: 10.1002/Cphc.201501041  0.592
2015 Winogradoff D, Zhao H, Dalal Y, Papoian GA. Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome. Scientific Reports. 5: 17038. PMID 26602160 DOI: 10.1038/Srep17038  0.77
2015 Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. Journal of the American Chemical Society. 137: 6245-53. PMID 25905561 DOI: 10.1021/Jacs.5B00235  0.717
2015 Zhao H, Dalal Y, Papoian GA. The Binding Landscapes of the H3/H4 and CENP-A/H4 Dimers Biophysical Journal. 108: 538a. DOI: 10.1016/J.Bpj.2014.11.2949  0.758
2015 Zhao H, Fushman D, Papoian GA. The Association Landscape of Ubiquitin Dimerization Biophysical Journal. 108: 519a. DOI: 10.1016/J.Bpj.2014.11.2848  0.653
2015 Komianos JE, Popov K, Papoian G. Simulating Complex Mechanochemistry of Actin Networks Biophysical Journal. 108: 452a. DOI: 10.1016/J.Bpj.2014.11.2468  0.32
2015 Winogradoff D, Echeverria I, Papoian G. The Acetylation Landscape of the H4 Histone Tail Biophysical Journal. 108: 388a. DOI: 10.1016/J.Bpj.2014.11.2128  0.426
2015 Wu H, Papoian G. Structural and Dynamic Analysis on Disordered H4 Histone Tail by Modified AWSEM-MD Biophysical Journal. 108: 388a. DOI: 10.1016/J.Bpj.2014.11.2127  0.461
2013 Ma D, Bettis SE, Hanson K, Minakova M, Alibabaei L, Fondrie W, Ryan DM, Papoian GA, Meyer TJ, Waters ML, Papanikolas JM. Interfacial energy conversion in Ru(II) polypyridyl-derivatized oligoproline assemblies on TiO2. Journal of the American Chemical Society. 135: 5250-3. PMID 23514453 DOI: 10.1021/Ja312143H  0.757
2013 Echeverria I, Makarov DE, Papoian G. Insight into the Molecular Origins of the Internal Friction in Unfolded Proteins Biophysical Journal. 104: 188a. DOI: 10.1016/J.Bpj.2012.11.1061  0.392
2013 Potoyan DA, Savelyev A, Papoian GA. Recent successes in coarse-grained modeling of DNA Wiley Interdisciplinary Reviews: Computational Molecular Science. 3: 69-83. DOI: 10.1002/wcms.1114  0.657
2012 Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG. Predictive energy landscapes for protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 109: 19244-9. PMID 23129648 DOI: 10.1073/Pnas.1216215109  0.721
2012 Potoyan DA, Papoian GA. Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17857-62. PMID 22988066 DOI: 10.1073/pnas.1201805109  0.729
2012 Zhuravlev PI, Lan Y, Minakova MS, Papoian GA. Theory of active transport in filopodia and stereocilia. Proceedings of the National Academy of Sciences of the United States of America. 109: 10849-54. PMID 22711803 DOI: 10.1073/Pnas.1200160109  0.75
2012 Wilger DJ, Bettis SE, Materese CK, Minakova M, Papoian GA, Papanikolas JM, Waters ML. Tunable energy transfer rates via control of primary, secondary, and tertiary structure of a coiled coil peptide scaffold. Inorganic Chemistry. 51: 11324-38. PMID 22679929 DOI: 10.1021/Ic300669T  0.738
2012 Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. The Journal of Physical Chemistry. B. 116: 8494-503. PMID 22545654 DOI: 10.1021/Jp212541Y  0.693
2012 Potoyan DA, Zhuravlev PI, Papoian GA. Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations. The Journal of Physical Chemistry. B. 116: 1709-15. PMID 22212071 DOI: 10.1021/jp209980b  0.686
2012 Davtyan A, Zheng W, Schafer N, Wolynes P, Papoian G. AWSEM-MD: Coarse-Grained Protein Structure Prediction using Physical Potentials and Bioinformatically Based Local Structure Biasing Biophysical Journal. 102: 619a. DOI: 10.1016/J.Bpj.2011.11.3373  0.733
2011 Savelyev A, Materese CK, Papoian GA. Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions? Journal of the American Chemical Society. 133: 19290-3. PMID 22039974 DOI: 10.1021/Ja207984Z  0.715
2011 Minakova M, Savelyev A, Papoian GA. Nonequilibrium water transport in a nonionic microemulsion system. The Journal of Physical Chemistry. B. 115: 6503-8. PMID 21528855 DOI: 10.1021/Jp201431U  0.742
2011 Potoyan DA, Papoian GA. Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. Journal of the American Chemical Society. 133: 7405-15. PMID 21517079 DOI: 10.1021/ja1111964  0.715
2011 Zhuravlev PI, Minakova M, Lan Y, Papoian GA. Myosin Motor Dynamics in Filopodia Biophysical Journal. 100: 596a. DOI: 10.1016/J.Bpj.2010.12.3433  0.748
2011 Bettis S, Wilger D, Materese C, Minakova M, Papoian G, Papanikolas JM, Waters ML. Energy transfer in ruthenium and osmium functionalized coiled-coil peptides Acs National Meeting Book of Abstracts.  0.537
2010 Oklejas V, Zong C, Papoian GA, Wolynes PG. Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice? Methods (San Diego, Calif.). 52: 84-90. PMID 20561998 DOI: 10.1016/J.Ymeth.2010.05.006  0.63
2010 Zhuravlev PI, Wu S, Potoyan DA, Rubinstein M, Papoian GA. Computing free energies of protein conformations from explicit solvent simulations. Methods (San Diego, Calif.). 52: 115-21. PMID 20493264 DOI: 10.1016/J.Ymeth.2010.05.003  0.679
2010 Potoyan D, Papoian G. Energy Landscape Analysis Reveals Residual Order in Histone Tail Dynamics Biophysical Journal. 98: 257a. DOI: 10.1016/J.Bpj.2009.12.1395  0.74
2009 Materese CK, Savelyev A, Papoian GA. Counterion atmosphere and hydration patterns near a nucleosome core particle. Journal of the American Chemical Society. 131: 15005-13. PMID 19778017 DOI: 10.1021/Ja905376Q  0.737
2009 Zhuravlev PI, Materese CK, Papoian GA. Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. The Journal of Physical Chemistry. B. 113: 8800-12. PMID 19453123 DOI: 10.1021/Jp810659U  0.747
2008 Materese CK, Goldmon CC, Papoian GA. Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions. Proceedings of the National Academy of Sciences of the United States of America. 105: 10659-64. PMID 18664578 DOI: 10.1073/Pnas.0801850105  0.724
2007 Lätzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. Journal of Molecular Biology. 367: 262-74. PMID 17257619 DOI: 10.1016/J.Jmb.2006.12.006  0.752
2006 Lan Y, Wolynes PG, Papoian GA. A variational approach to the stochastic aspects of cellular signal transduction. The Journal of Chemical Physics. 125: 124106. PMID 17014165 DOI: 10.1063/1.2353835  0.403
2006 Zong C, Papoian GA, Ulander J, Wolynes PG. Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins. Journal of the American Chemical Society. 128: 5168-76. PMID 16608353 DOI: 10.1021/Ja058589V  0.618
2004 Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Water in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 101: 3352-7. PMID 14988499 DOI: 10.1073/Pnas.0307851100  0.484
2004 Levy Y, Papoian GA, Onuchic JN, Wolynes PG. Energy landscape analysis of protein dimers Israel Journal of Chemistry. 44: 281-297. DOI: 10.1560/Xgcb-Wuhn-Jrjc-Bv0Y  0.505
2003 Papoian GA, Ulander J, Wolynes PG. Role of water mediated interactions in protein-protein recognition landscapes. Journal of the American Chemical Society. 125: 9170-8. PMID 15369374 DOI: 10.1021/Ja034729U  0.459
2003 Papoian GA, Wolynes PG. The physics and bioinformatics of binding and folding-an energy landscape perspective. Biopolymers. 68: 333-49. PMID 12601793 DOI: 10.1002/Bip.10286  0.505
2003 Papoian GA, DeGrado WF, Klein ML. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor. Journal of the American Chemical Society. 125: 560-9. PMID 12517172 DOI: 10.1021/Ja028161L  0.409
2001 Ienco A, Hoffmann R, Papoian G. Electron-rich bonding and the importance of s,p mixing as one moves across a period: a lesson from the LiSn system. Journal of the American Chemical Society. 123: 2317-25. PMID 11456880 DOI: 10.1021/Ja0032576  0.423
2001 Papoian G, Hoffmann R. Electron-rich rods as building blocks for Sb strips and Te sheets. Journal of the American Chemical Society. 123: 6600-8. PMID 11439046 DOI: 10.1021/Ja003420X  0.39
2000 Papoian G, Nørskov JK, Hoffmann R. A comparative theoretical study of the hydrogen, methyl, and ethyl chemisorption on the Pt(111) surface Journal of the American Chemical Society. 122: 4129-4144. DOI: 10.1021/Ja993483J  0.426
2000 Papoian GA, Hoffmann R. Hypervalent bonding in one, two, and three dimensions: Extending the Zintl-Klemm concept to nonclassical electron-rich networks Angewandte Chemie - International Edition. 39: 2408-2448. DOI: 10.1002/1521-3773(20000717)39:14<2408::Aid-Anie2408>3.0.Co;2-U  0.325
2000 Seo D, Papoian G, Hoffmann R. Generalized perturbational molecular orbital (PMO) theory*Dedicated to our friend, Mike Zerner. International Journal of Quantum Chemistry. 77: 408. DOI: 10.1002/(Sici)1097-461X(2000)77:1<408::Aid-Qua41>3.3.Co;2-T  0.562
2000 Seo DK, Papoian G, Hoffmann R. Generalized perturbational molecular orbital (PMO) theory International Journal of Quantum Chemistry. 77: 408-420. DOI: 10.1002/(Sici)1097-461X(2000)77:1<408::Aid-Qua41>3.0.Co;2-1  0.388
1999 Glassey WV, Papoian GA, Hoffmann R. Total energy partitioning within a one-electron formalism: A Hamilton population study of surface-CO interaction in the c(2x2)-CO/Ni(100) chemisorption system Journal of Chemical Physics. 111: 893-910.  0.744
1998 Papoian G, Hoffmann R. Building up Complexity from Strips and Sheets: The Electronic Structure of the La12Mn2Sb30Alloy Journal of Solid State Chemistry. 139: 8-21. DOI: 10.1006/Jssc.1998.7773  0.445
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