Rohit V. Pappu - Publications

Biomedical Engineering Washington University, Saint Louis, St. Louis, MO 
General Biophysics, Condensed Matter Physics

115 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
2021 Posey AE, Ruff KM, Lalmansingh JM, Kandola TS, Lange JJ, Halfmann R, Pappu RV. Mechanistic inferences from analysis of measurements of protein phase transitions in live cells. Journal of Molecular Biology. 166848. PMID 33539877 DOI: 10.1016/j.jmb.2021.166848  0.88
2021 Lorenzini M, Burel S, Lesage A, Wagner E, Charrière C, Chevillard PM, Evrard B, Maloney D, Ruff KM, Pappu RV, Wagner S, Nerbonne JM, Silva JR, Townsend RR, Maier LS, et al. Proteomic and functional mapping of cardiac NaV1.5 channel phosphorylation sites. The Journal of General Physiology. 153. PMID 33410863 DOI: 10.1085/jgp.202012646  0.88
2020 Lazar T, Martínez-Pérez E, Quaglia F, Hatos A, Chemes LB, Iserte JA, Méndez NA, Garrone NA, Saldaño TE, Marchetti J, Rueda AJV, Bernadó P, Blackledge M, Cordeiro TN, Fagerberg E, ... ... Pappu RV, et al. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research. PMID 33305318 DOI: 10.1093/nar/gkaa1021  0.88
2020 Choi JM, Hyman AA, Pappu RV. Generalized models for bond percolation transitions of associative polymers. Physical Review. E. 102: 042403. PMID 33212590 DOI: 10.1103/PhysRevE.102.042403  0.88
2020 Guillén-Boixet J, Kopach A, Holehouse AS, Wittmann S, Jahnel M, Schlüßler R, Kim K, Trussina IREA, Wang J, Mateju D, Poser I, Maharana S, Ruer-Gruß M, Richter D, Zhang X, ... ... Pappu RV, et al. RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation. Cell. 181: 346-361.e17. PMID 32302572 DOI: 10.1016/j.cell.2020.03.049  0.56
2020 Greig JA, Nguyen TA, Lee M, Holehouse AS, Posey AE, Pappu RV, Jedd G. Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation. Molecular Cell. PMID 32048997 DOI: 10.1016/j.molcel.2020.01.025  0.56
2020 Martin EW, Holehouse AS, Peran I, Farag M, Incicco JJ, Bremer A, Grace CR, Soranno A, Pappu RV, Mittag T. Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science (New York, N.Y.). 367: 694-699. PMID 32029630 DOI: 10.1126/science.aaw8653  0.56
2020 Choi JM, Holehouse AS, Pappu RV. Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions. Annual Review of Biophysics. PMID 32004090 DOI: 10.1146/annurev-biophys-121219-081629  0.88
2019 Choi JM, Dar F, Pappu RV. LASSI: A lattice model for simulating phase transitions of multivalent proteins. Plos Computational Biology. 15: e1007028. PMID 31634364 DOI: 10.1371/journal.pcbi.1007028  0.88
2019 Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC. Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. Molecular Cell. PMID 31421981 DOI: 10.1016/j.molcel.2019.06.044  0.56
2019 Cohan MC, Ruff KM, Pappu RV. Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins. Protein Engineering, Design & Selection : Peds. PMID 31375817 DOI: 10.1093/protein/gzz014  0.88
2019 Bai W, Sargent CJ, Choi JM, Pappu RV, Zhang F. Covalently-assembled single-chain protein nanostructures with ultra-high stability. Nature Communications. 10: 3317. PMID 31346167 DOI: 10.1038/s41467-019-11285-8  0.88
2019 Peran I, Holehouse AS, Carrico IS, Pappu RV, Bilsel O, Raleigh DP. Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions. Proceedings of the National Academy of Sciences of the United States of America. PMID 31167941 DOI: 10.1073/pnas.1818206116  0.56
2019 Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD. Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proceedings of the National Academy of Sciences of the United States of America. PMID 30926670 DOI: 10.1073/pnas.1821038116  0.56
2019 Beveridge R, Migas LG, Das RK, Pappu RV, Kriwacki RW, Barran PE. Ion mobility mass spectrometry uncovers the impact of the patterning of oppositely charged residues on the conformational distributions of intrinsically disordered proteins. Journal of the American Chemical Society. PMID 30823702 DOI: 10.1021/jacs.8b13483  0.56
2019 Choi JM, Pappu RV. Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics. Journal of Chemical Theory and Computation. PMID 30633502 DOI: 10.1021/acs.jctc.8b00573  0.88
2018 Choi JM, Pappu RV. Experimentally derived and computationally optimized backbone conformational statistics for blocked amino acids. Journal of Chemical Theory and Computation. PMID 30516982 DOI: 10.1021/acs.jctc.8b00572  0.88
2018 Posey AE, Holehouse AS, Pappu RV. Phase Separation of Intrinsically Disordered Proteins. Methods in Enzymology. 611: 1-30. PMID 30471685 DOI: 10.1016/bs.mie.2018.09.035  0.56
2018 Ruff KM, Pappu RV, Holehouse AS. Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations. Current Opinion in Structural Biology. 56: 1-10. PMID 30439585 DOI: 10.1016/  0.88
2018 Fuertes G, Banterle N, Ruff KM, Chowdhury A, Pappu RV, Svergun DI, Lemke EA. Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science (New York, N.Y.). 361. PMID 30166461 DOI: 10.1126/science.aau8230  0.88
2018 Yoo TY, Choi JM, Conway W, Yu CH, Pappu RV, Needleman DJ. Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments. Elife. 7. PMID 30044223 DOI: 10.7554/eLife.36392  0.88
2018 Mirbaha H, Chen D, Morazova OA, Ruff KM, Sharma AM, Liu X, Goodarzi M, Pappu RV, Colby DW, Mirzaei H, Joachimiak LA, Diamond MI. Inert and seed-competent tau monomers suggest structural origins of aggregation. Elife. 7. PMID 29988016 DOI: 10.7554/eLife.36584  0.88
2018 Wang J, Choi JM, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA. A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins. Cell. PMID 29961577 DOI: 10.1016/j.cell.2018.06.006  0.88
2018 Ruff KM, Roberts S, Chilkoti A, Pappu RV. Advances in Understanding Stimulus Responsive Phase Behavior of Intrinsically Disordered Protein Polymers. Journal of Molecular Biology. PMID 29949750 DOI: 10.1016/j.jmb.2018.06.031  0.88
2018 Mittal A, Holehouse AS, Cohan MC, Pappu RV. Equation Chapter 1 Section 1Sequence-To-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins. Journal of Molecular Biology. PMID 29763584 DOI: 10.1016/j.jmb.2018.05.012  0.56
2018 Newcombe EA, Ruff KM, Sethi A, Ormsby AR, Ramdzan YM, Fox A, Purcell AW, Gooley PR, Pappu RV, Hatters DM. Tadpole-like conformations of huntingtin exon 1 are characterized by conformational heterogeneity that persists regardless of polyglutamine length. Journal of Molecular Biology. PMID 29627459 DOI: 10.1016/j.jmb.2018.03.031  0.88
2018 Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA. A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Systems. PMID 29525204 DOI: 10.1016/j.cels.2018.01.015  0.56
2018 Garai K, Posey AE, Li X, Buxbaum JN, Pappu RV. Inhibition of Amyloid Beta Fibril Formation by Monomeric Human Transthyretin. Protein Science : a Publication of the Protein Society. PMID 29498118 DOI: 10.1002/pro.3396  0.88
2018 Posey AE, Ruff KM, Harmon TS, Crick SL, Li A, Diamond MI, Pappu RV. Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers. The Journal of Biological Chemistry. PMID 29358329 DOI: 10.1074/jbc.RA117.000357  1
2018 Holehouse AS, Pappu RV. Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. Annual Review of Biophysics. PMID 29345991 DOI: 10.1146/annurev-biophys-070317-032838  0.56
2018 Holehouse AS, Pappu RV. Functional Implications of Intracellular Phase Transitions. Biochemistry. PMID 29323488 DOI: 10.1021/acs.biochem.7b01136  0.56
2018 Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S. Phase separation of a yeast prion protein promotes cellular fitness. Science (New York, N.Y.). 359. PMID 29301985 DOI: 10.1126/science.aao5654  0.56
2017 Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. Journal of Cell Science. PMID 29133588 DOI: 10.1242/jcs.206854  0.56
2017 Harmon TS, Holehouse AS, Rosen MK, Pappu RV. Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins. Elife. 6. PMID 29091028 DOI: 10.7554/eLife.30294  0.56
2017 Sherry KP, Das RK, Pappu RV, Barrick D. Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078291 DOI: 10.1073/pnas.1706083114  0.56
2017 Wei MT, Elbaum-Garfinkle S, Holehouse AS, Chen CC, Feric M, Arnold CB, Priestley RD, Pappu RV, Brangwynne CP. Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Nature Chemistry. 9: 1118-1125. PMID 29064502 DOI: 10.1038/nchem.2803  0.56
2017 Holehouse AS, Pappu RV. FUS Zigzags Its Way to Cross Beta. Cell. 171: 499-500. PMID 29053965 DOI: 10.1016/j.cell.2017.10.007  0.56
2017 Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, et al. Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proceedings of the National Academy of Sciences of the United States of America. PMID 28716919 DOI: 10.1073/pnas.1704692114  0.88
2017 Harmon TS, Holehouse AS, Pappu RV. To Mix, or To Demix, That Is the Question. Biophysical Journal. 112: 565-567. PMID 28256216 DOI: 10.1016/j.bpj.2016.12.031  0.56
2017 Kalas V, Pinkner JS, Hannan TJ, Hibbing ME, Dodson KW, Holehouse AS, Zhang H, Tolia NH, Gross ML, Pappu RV, Janetka J, Hultgren SJ. Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions. Science Advances. 3: e1601944. PMID 28246638 DOI: 10.1126/sciadv.1601944  0.56
2017 Holehouse AS, Das RK, Ahad JN, Richardson MO, Pappu RV. CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins. Biophysical Journal. 112: 16-21. PMID 28076807 DOI: 10.1016/j.bpj.2016.11.3200  0.56
2016 Martin EW, Holehouse AS, Grace CR, Hughes A, Pappu RV, Mittag T. Sequence determinants of the conformational properties of an intrinsically disordered protein prior to and upon multisite phosphorylation. Journal of the American Chemical Society. PMID 27807972 DOI: 10.1021/jacs.6b10272  0.56
2016 Pak CW, Kosno M, Holehouse AS, Padrick SB, Mittal A, Ali R, Yunus AA, Liu DR, Pappu RV, Rosen MK. Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein. Molecular Cell. 63: 72-85. PMID 27392146 DOI: 10.1016/j.molcel.2016.05.042  0.56
2016 Das RK, Huang Y, Phillips AH, Kriwacki RW, Pappu RV. Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling. Proceedings of the National Academy of Sciences of the United States of America. PMID 27140628 DOI: 10.1073/pnas.1516277113  1
2015 Ruff KM, Harmon TS, Pappu RV. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences. The Journal of Chemical Physics. 143: 243123. PMID 26723608 DOI: 10.1063/1.4935066  0.88
2015 Banjade S, Wu Q, Mittal A, Peeples WB, Pappu RV, Rosen MK. Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck. Proceedings of the National Academy of Sciences of the United States of America. PMID 26553976 DOI: 10.1073/pnas.1508778112  1
2015 Holehouse AS, Pappu RV. Protein polymers: Encoding phase transitions. Nature Materials. 14: 1083-4. PMID 26490213 DOI: 10.1038/nmat4459  1
2015 Das RK, Ruff KM, Pappu RV. Relating sequence encoded information to form and function of intrinsically disordered proteins. Current Opinion in Structural Biology. 32: 102-12. PMID 25863585 DOI: 10.1016/  1
2015 Pappu RV. Cell signaling, division, and organization mediated by intrinsically disordered proteins. Seminars in Cell & Developmental Biology. 37: 1-2. PMID 25703796 DOI: 10.1016/j.semcdb.2015.01.003  1
2015 Diamond MI, Cai S, Boudreau A, Carey CJ, Lyle N, Pappu RV, Swamidass SJ, Bissell M, Piwnica-Worms H, Shao J. Subcellular localization and Ser-137 phosphorylation regulate tumor-suppressive activity of profilin-1. The Journal of Biological Chemistry. 290: 9075-86. PMID 25681442 DOI: 10.1074/jbc.M114.619874  1
2015 Holehouse AS, Garai K, Lyle N, Vitalis A, Pappu RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. Journal of the American Chemical Society. 137: 2984-95. PMID 25664638 DOI: 10.1021/ja512062h  1
2015 Kozlov AG, Weiland E, Mittal A, Waldman V, Antony E, Fazio N, Pappu RV, Lohman TM. Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA. Journal of Molecular Biology. 427: 763-74. PMID 25562210 DOI: 10.1016/j.jmb.2014.12.020  1
2015 Brangwynne CP, Tompa P, Pappu RV. Polymer physics of intracellular phase transitions Nature Physics. 11: 899-904. DOI: 10.1038/nphys3532  1
2014 Ripaud L, Chumakova V, Antonin M, Hastie AR, Pinkert S, Körner R, Ruff KM, Pappu RV, Hornburg D, Mann M, Hartl FU, Hipp MS. Overexpression of Q-rich prion-like proteins suppresses polyQ cytotoxicity and alters the polyQ interactome. Proceedings of the National Academy of Sciences of the United States of America. 111: 18219-24. PMID 25489109 DOI: 10.1073/pnas.1421313111  1
2014 Ruff KM, Khan SJ, Pappu RV. A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences. Biophysical Journal. 107: 1226-35. PMID 25185558 DOI: 10.1016/j.bpj.2014.07.019  1
2014 Pappu RV. Frozen in beta. Biophysical Journal. 107: 795-7. PMID 25140412 DOI: 10.1016/j.bpj.2014.07.007  1
2014 Mittal A, Lyle N, Harmon TS, Pappu RV. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins. Journal of Chemical Theory and Computation. 10: 3550-3562. PMID 25136274 DOI: 10.1021/ct5002297  1
2014 Xu W, Edwards MR, Borek DM, Feagins AR, Mittal A, Alinger JB, Berry KN, Yen B, Hamilton J, Brett TJ, Pappu RV, Leung DW, Basler CF, Amarasinghe GK. Ebola virus VP24 targets a unique NLS binding site on karyopherin alpha 5 to selectively compete with nuclear import of phosphorylated STAT1. Cell Host & Microbe. 16: 187-200. PMID 25121748 DOI: 10.1016/j.chom.2014.07.008  1
2014 Vitalis A, Pappu RV. A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. The Journal of Chemical Physics. 141: 034105. PMID 25053299 DOI: 10.1063/1.4887339  1
2014 Tubbs AT, Dorsett Y, Chan E, Helmink B, Lee BS, Hung P, George R, Bredemeyer AL, Mittal A, Pappu RV, Chowdhury D, Mosammaparast N, Krangel MS, Sleckman BP. KAP-1 promotes resection of broken DNA ends not protected by γ-H2AX and 53BP1 in G₁-phase lymphocytes. Molecular and Cellular Biology. 34: 2811-21. PMID 24842905 DOI: 10.1128/MCB.00441-14  1
2014 van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, et al. Classification of intrinsically disordered regions and proteins. Chemical Reviews. 114: 6589-631. PMID 24773235 DOI: 10.1021/cr400525m  1
2014 Luan B, Lyle N, Pappu RV, Raleigh DP. Denatured state ensembles with the same radii of gyration can form significantly different long-range contacts. Biochemistry. 53: 39-47. PMID 24280003 DOI: 10.1021/bi4008337  1
2013 Crick SL, Ruff KM, Garai K, Frieden C, Pappu RV. Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation. Proceedings of the National Academy of Sciences of the United States of America. 110: 20075-80. PMID 24282292 DOI: 10.1073/pnas.1320626110  1
2013 Lyle N, Das RK, Pappu RV. A quantitative measure for protein conformational heterogeneity. The Journal of Chemical Physics. 139: 121907. PMID 24089719 DOI: 10.1063/1.4812791  1
2013 Das RK, Pappu RV. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proceedings of the National Academy of Sciences of the United States of America. 110: 13392-7. PMID 23901099 DOI: 10.1073/pnas.1304749110  1
2013 Meng W, Luan B, Lyle N, Pappu RV, Raleigh DP. The denatured state ensemble contains significant local and long-range structure under native conditions: analysis of the N-terminal domain of ribosomal protein L9. Biochemistry. 52: 2662-71. PMID 23480024 DOI: 10.1021/bi301667u  1
2013 Meng W, Lyle N, Luan B, Raleigh DP, Pappu RV. Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 110: 2123-8. PMID 23341588 DOI: 10.1073/pnas.1216979110  1
2013 Mao AH, Lyle N, Pappu RV. Describing sequence-ensemble relationships for intrinsically disordered proteins. The Biochemical Journal. 449: 307-18. PMID 23240611 DOI: 10.1042/BJ20121346  1
2013 Das RK, Mittal A, Pappu RV. How is functional specificity achieved through disordered regions of proteins? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 35: 17-22. PMID 23138868 DOI: 10.1002/bies.201200115  1
2013 Crick SL, Ruff KM, Garai K, Frieden C, Pappu RV. Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation Proceedings of the National Academy of Sciences of the United States of America. 110: 20075-20080. DOI: 10.1073/pnas.1320626110  1
2012 Babu MM, Kriwacki RW, Pappu RV. Structural biology. Versatility from protein disorder. Science (New York, N.Y.). 337: 1460-1. PMID 22997313 DOI: 10.1126/science.1228775  1
2012 Mao AH, Pappu RV. Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions. The Journal of Chemical Physics. 137: 064104. PMID 22897252 DOI: 10.1063/1.4742068  1
2012 Das RK, Mao AH, Pappu RV. Unmasking functional motifs within disordered regions of proteins. Science Signaling. 5: pe17. PMID 22510467 DOI: 10.1126/scisignal.2003091  1
2012 Radhakrishnan A, Vitalis A, Mao AH, Steffen AT, Pappu RV. Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. The Journal of Physical Chemistry. B. 116: 6862-71. PMID 22329658 DOI: 10.1021/jp212637r  1
2012 Das RK, Crick SL, Pappu RV. N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins. Journal of Molecular Biology. 416: 287-99. PMID 22226835 DOI: 10.1016/j.jmb.2011.12.043  1
2012 Crick SL, Pappu RV. Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins Protein and Peptide Folding, Misfolding, and Non-Folding. 413-440. DOI: 10.1002/9781118183373.ch14  1
2011 Halfmann R, Alberti S, Krishnan R, Lyle N, O'Donnell CW, King OD, Berger B, Pappu RV, Lindquist S. Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. Molecular Cell. 43: 72-84. PMID 21726811 DOI: 10.1016/j.molcel.2011.05.013  1
2011 Vitalis A, Pappu RV. Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides. Biophysical Chemistry. 159: 14-23. PMID 21530061 DOI: 10.1016/j.bpc.2011.04.006  1
2011 Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for cancer nanotechnology research. Journal of Biomedical Informatics. 44: 59-74. PMID 20211274 DOI: 10.1016/j.jbi.2010.03.001  1
2011 Mao AH, Pappu RV. Exact recording of metropolis-hastings-class Monte Carlo simulations using one bit per sample Computer Physics Communications. 182: 1452-1454. DOI: 10.1016/j.cpc.2011.03.013  1
2010 Wyczalkowski MA, Vitalis A, Pappu RV. New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision. The Journal of Physical Chemistry. B. 114: 8166-80. PMID 20503993 DOI: 10.1021/jp103050u  1
2010 Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America. 107: 8183-8. PMID 20404210 DOI: 10.1073/pnas.0911107107  1
2010 Williamson TE, Vitalis A, Crick SL, Pappu RV. Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin. Journal of Molecular Biology. 396: 1295-309. PMID 20026071 DOI: 10.1016/j.jmb.2009.12.017  1
2009 Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in Enzymology. 469: 411-32. PMID 20946801 DOI: 10.1016/S0076-6879(09)69020-0  1
2009 Vitalis A, Pappu RV. Methods for Monte Carlo simulations of biomacromolecules. Annual Reports in Computational Chemistry. 5: 49-76. PMID 20428473 DOI: 10.1016/S1574-1400(09)00503-9  1
2009 Thomas DG, Pappu RV, Baker NA. Ontologies for cancer nanotechnology research. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 4158-61. PMID 19964619 DOI: 10.1109/IEMBS.2009.5333941  1
2009 Hu X, Crick SL, Bu G, Frieden C, Pappu RV, Lee JM. Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide Proceedings of the National Academy of Sciences of the United States of America. 106: 20324-20329. PMID 19910533 DOI: 10.1073/pnas.0911281106  1
2009 Lashuel HA, Pappu RV. Amyloids go genomic: insights regarding the sequence determinants of prion formation from genome-wide studies. Chembiochem : a European Journal of Chemical Biology. 10: 1951-4. PMID 19598186 DOI: 10.1002/cbic.200900373  1
2009 Vitalis A, Lyle N, Pappu RV. Thermodynamics of beta-sheet formation in polyglutamine. Biophysical Journal. 97: 303-11. PMID 19580768 DOI: 10.1016/j.bpj.2009.05.003  1
2009 Chen AA, Draper DE, Pappu RV. Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. Journal of Molecular Biology. 390: 805-19. PMID 19482035 DOI: 10.1016/j.jmb.2009.05.071  1
2009 Pappu RV, Nussinov R. Protein folding: lessons learned and new frontiers. Preface. Physical Biology. 6: 010301. PMID 19208944 DOI: 10.1088/1478-3975/6/1/010301  1
2009 Vitalis A, Pappu RV. ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. Journal of Computational Chemistry. 30: 673-99. PMID 18506808 DOI: 10.1002/jcc.21005  1
2008 Vitalis A, Wang X, Pappu RV. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization. Journal of Molecular Biology. 384: 279-97. PMID 18824003 DOI: 10.1016/j.jmb.2008.09.026  1
2008 Tran HT, Mao A, Pappu RV. Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. Journal of the American Chemical Society. 130: 7380-92. PMID 18481860 DOI: 10.1021/ja710446s  1
2008 Wyczalkowski MA, Pappu RV. Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 026104. PMID 18352087 DOI: 10.1103/PhysRevE.77.026104  1
2008 Pappu RV, Wang X, Vitalis A, Crick SL. A polymer physics perspective on driving forces and mechanisms for protein aggregation. Archives of Biochemistry and Biophysics. 469: 132-41. PMID 17931593 DOI: 10.1016/  1
2008 Wyczalkowski MA, Pappu RV. Publisher's Note: Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange (Physical Review e (2008) 77 (026104)) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 77. DOI: 10.1103/PhysRevE.77.029905  1
2007 Chen AA, Pappu RV. Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. The Journal of Physical Chemistry. B. 111: 11884-7. PMID 17887792 DOI: 10.1021/jp0765392  1
2007 Vitalis A, Wang X, Pappu RV. Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories. Biophysical Journal. 93: 1923-37. PMID 17526581 DOI: 10.1529/biophysj.107.110080  1
2007 Chen AA, Pappu RV. Quantitative characterization of ion pairing and cluster formation in strong 1:1 electrolytes. The Journal of Physical Chemistry. B. 111: 6469-78. PMID 17518490 DOI: 10.1021/jp0708547  1
2006 Crick SL, Jayaraman M, Frieden C, Wetzel R, Pappu RV. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions Proceedings of the National Academy of Sciences of the United States of America. 103: 16764-16769. PMID 17075061 DOI: 10.1073/pnas.0608175103  1
2006 Tran HT, Pappu RV. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophysical Journal. 91: 1868-86. PMID 16766618 DOI: 10.1529/biophysj.106.086264  1
2006 Wang X, Vitalis A, Wyczalkowski MA, Pappu RV. Characterizing the conformational ensemble of monomeric polyglutamine. Proteins. 63: 297-311. PMID 16299774 DOI: 10.1002/prot.20761  1
2005 Tran HT, Wang X, Pappu RV. Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins. Biochemistry. 44: 11369-80. PMID 16114874 DOI: 10.1021/bi050196l  1
2004 Patriciu A, Chirikjian GS, Pappu RV. Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints. The Journal of Chemical Physics. 121: 12708-20. PMID 15606297 DOI: 10.1063/1.1821492  1
2004 Drozdov AN, Grossfield A, Pappu RV. Role of solvent in determining conformational preferences of alanine dipeptide in water. Journal of the American Chemical Society. 126: 2574-81. PMID 14982467 DOI: 10.1021/ja039051x  1
2002 Pappu RV, Rose GD. A simple model for polyproline II structure in unfolded states of alanine-based peptides. Protein Science : a Publication of the Protein Society. 11: 2437-55. PMID 12237465 DOI: 10.1110/ps.0217402  1
2000 Pappu RV, Srinivasan R, Rose GD. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding Proceedings of the National Academy of Sciences of the United States of America. 97: 12565-12570. PMID 11070081 DOI: 10.1073/pnas.97.23.12565  1
2000 Hart RK, Pappu RV, Ponder JW. Exploring the Similarities between Potential Smoothing and Simulated Annealing Journal of Computational Chemistry. 21: 531-552.  1
1999 Pappu RV. Review of the Fourth Johns Hopkins Protein Folding Meeting Proteins: Structure, Function and Genetics. 36: 263-269. PMID 10409820 DOI: 10.1002/(SICI)1097-0134(19990815)36:3<263::AID-PROT1>3.0.CO;2-Q  1
1999 Pappu RV, Marshall GR, Ponder JW. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nature Structural Biology. 6: 50-5. PMID 9886292 DOI: 10.1038/4922  1
1998 Huang ES, Koehl P, Levitt M, Pappu RV, Ponder JW. Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods. Proteins. 33: 204-17. PMID 9779788 DOI: 10.1002/(SICI)1097-0134(19981101)33:2<204::AID-PROT5>3.0.CO;2-I  1
1998 Pappu RV, Weaver DL. The early folding kinetics of apomyoglobin Protein Science. 7: 480-490. PMID 9521125  1
1998 Pappu RV, Hart RK, Ponder JW. Analysis and application of potential energy smoothing and search methods for global optimization Journal of Physical Chemistry B. 102: 9725-9742.  1
1996 Pappu RV, Schneller WJ, Weaver DL. Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties Journal of Computational Chemistry. 17: 1033-1055.  1
Show low-probability matches.