• 2024
  Germain Niogret, Alix Bouvier-Müller, Chiara Figazzolo, Jack M. Joyce, Frédéric Bonhomme, Patrick England, Olena Mayboroda, Riccardo Pellarin, Gilles Gasser, James H. R. Tucker, Julian A. Tanner, G. Paul Savage, Marcel Hollenstein*, Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis, ChemBioChem 2024, 25, e202300539.
• 2022
  Bouvier G, Bardiaux B, Pellarin R, Rapisarda C, Nilges M, , Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution., Biomolecules 2022 Sep; 12(9): .
• 2021
  Rey M, Dhenin J, Kong Y, Nouchikian L, Filella I, Duchateau M, Dupré M, Pellarin R, Duménil G, Chamot-Rooke J, , Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions., Anal Chem 2021 Feb; (): .
• 2019
  Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R, Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling, Structure 27 (2019) 175-188.
• 2018
  Bonomi M, Pellarin R, Vendruscolo M, Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy, Biophys. J. 2018 Apr;114(7):1604-1613.
• 2018
  Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP, Integrative structure and functional anatomy of a nuclear pore complex, Nature 2018 03;555(7697):475-482.
• 2018
  Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A, Integrative structure modeling with the Integrative Modeling Platform, Protein Sci. 2018 01;27(1):245-258.
• 2017
  Obayashi E, Luna RE, Nagata T, Martin-Marcos P, Hiraishi H, Singh CR, Erzberger JP, Zhang F, Arthanari H, Morris J, Pellarin R, Moore C, Harmon I, Papadopoulos E, Yoshida H, Nasr ML, Unzai S, Thompson B, Aube E, Hustak S, Stengel F, Dagraca E, Ananbandam A, Gao P, Urano T, Hinnebusch AG, Wagner G, Asano K, Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5, Cell Rep 2017 03;18(11):2651-2663.
• 2016
  Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A, A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions, J Phys Chem B 2017 04;121(15):3493-3501.
• 2016
  Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP, Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform, Cell 2016 11;167(5):1215-1228.e25.
• 2016
  Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J, Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling, Mol. Cell Proteomics 2016 08;15(8):2730-43.
• 2015
  Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J, Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH, Mol. Cell 2015 Sep;59(5):794-806.
• 2014
  Schneidman-Duhovny D, Pellarin R, Sali A, Uncertainty in integrative structural modeling, Curr. Opin. Struct. Biol. 2014 Oct;28:96-104.
• 2014
  Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N, Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex, Cell 2014 Aug;158(5):1123-35.
• 2014
  Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT, Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex, Mol. Cell Proteomics 2014 Nov;13(11):2927-43.
• 2014
  Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F, Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling, J. Mol. Biol. 2014 Nov;426(22):3713-28.
• 2014
  Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A, Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data, Mol. Cell Proteomics 2014 Nov;13(11):2812-23.
• 2014
  Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF, Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ, Structure 2014 Sep;22(9):1239-1251.
• 2014
  Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S, Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway, Mol. Cell Proteomics 2014 Nov;13(11):2855-70.
• 2014
  Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA, Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone, J. Mol. Biol. 2014 Jun;426(12):2393-404.
• 2014
  Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A, Modeling of proteins and their assemblies with the Integrative Modeling Platform, Methods Mol. Biol. 2014;1091:277-95.
• 2013
  Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A, Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation, J Phys Chem B 2013 Feb;117(6):1780-9.
• 2012
  Alfarano P, Varadamsetty G, Ewald C, Parmeggiani F, Pellarin R, Zerbe O, Plückthun A, Caflisch A, Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy, Protein Sci. 2012 Sep;21(9):1298-314.
• 2012
  Waldauer SA, Hassan S, Paoli B, Donaldson PM, Pfister R, Hamm P, Caflisch A, Pellarin R, Photocontrol of reversible amyloid formation with a minimal-design peptide, J Phys Chem B 2012 Aug;116(30):8961-73.
• 2011
  Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E, Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue, ACS Chem. Biol. 2011 Nov;6(11):1265-76.
• 2010
  Pellarin R, Schuetz P, Guarnera E, Caflisch A, Amyloid fibril polymorphism is under kinetic control, J. Am. Chem. Soc. 2010 Oct;132(42):14960-70.
• 2010
  Scherzer-Attali R, Pellarin R, Convertino M, Frydman-Marom A, Egoz-Matia N, Peled S, Levy-Sakin M, Shalev DE, Caflisch A, Gazit E, Segal D, Complete phenotypic recovery of an Alzheimer’s disease model by a quinone-tryptophan hybrid aggregation inhibitor, PLoS ONE 2010;5(6):e11101.
• 2009
  Guarnera E, Pellarin R, Caflisch A, How does a simplified-sequence protein fold?, Biophys. J. 2009 Sep;97(6):1737-46.
• 2009
  Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A, 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation?, Protein Sci. 2009 Apr;18(4):792-800.
• 2008
  Friedman R, Pellarin R, Caflisch A, Amyloid aggregation on lipid bilayers and its impact on membrane permeability, J. Mol. Biol. 2009 Mar;387(2):407-15.
• 2007
  Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A, Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core, J. Mol. Biol. 2008 Mar;376(5):1282-304.
• 2007
  Pellarin R, Guarnera E, Caflisch A, Pathways and intermediates of amyloid fibril formation, J. Mol. Biol. 2007 Dec;374(4):917-24.
• 2006
  Pellarin R, Caflisch A, Interpreting the aggregation kinetics of amyloid peptides, J. Mol. Biol. 2006 Jul;360(4):882-92.
• 2005
  Tartaglia GG, Cavalli A, Pellarin R, Caflisch A, Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences, Protein Sci. 2005 Oct;14(10):2723-34.
• 2005
  Tartaglia GG, Pellarin R, Cavalli A, Caflisch A, Organism complexity anti-correlates with proteomic beta-aggregation propensity, Protein Sci. 2005 Oct;14(10):2735-40.
• 2004
  Gorfe AA, Pellarin R, Caflisch A, Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations, J. Am. Chem. Soc. 2004 Nov;126(46):15277-86.
• 2004
  Tartaglia GG, Cavalli A, Pellarin R, Caflisch A, The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates, Protein Sci. 2004 Jul;13(7):1939-41.