top of page

Publications

  1. Monomer binding modes of small molecules that modulate the amyloid aggregation kinetics of hIAPP.                                                                 M Garcia, KM Reid, P Robustelli  https://doi.org/10.1101/2025.09.22.677832                                                                                                              bioRxiv (2025)

  2. Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe                                                                         TR Sisk, S Olsson, P Robustelli.  https://doi.org/10.1101/2025.04.26.650781                                                                                                    Journal of Chemical Theory and Computation (In Press) (2025)

  3. Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution,                                                            K Borthakur, TR Sisk, FP Panei, M Bonomi, P Robustelli.  https://doi.org/10.1101/2024.10.04.616700                                                                      Nature Communications , 16(1), 9036 (2025)

  4.  Performing all-atom molecular dynamics simulations of intrinsically disordered proteins with replica exchange solute tempering                     JK Koneru, KM Reid, P Robustelli. https://doi.org/10.48550/arXiv.2505.01860                                                                                                     (Accepted Book Chapter - Methods in Molecular Biology: Biomolecular Simulations) (2025)

  5.  Ensemble docking for intrinsically disordered protein                                                                                                                                                 A ​Dhar, TR Sisk, P Robustelli   https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c00370                                                                                     Journal of Chemical Information and Modeling, 65, 13, 6847-6860 (2025) 

  6. Covalent adducts formed by the androgen receptor transactivation domain and small molecule drugs remain disordered                             . J Zhu &  P Robustelli.  https://pubs.acs.org/doi/10.1021/acs.jcim.5c00833                                                                                                                  Journal of Chemical Informatics and Modeling, 65, 12, 6221–6237  (2025) 

  7. Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields.                                                                              C Cavender, D Case, J Chen, L Chong, D Keedy, K Lindorff-Larsen, D Mobley, O Ollila, C Oostenbrink, P Robustelli, V Voelz, M Wall, D Wych, M Gilson https://livecomsjournal.org/index.php/livecoms/article/view/v6i1e3871                                                                                         Living Journal of Computational Science, Vol. 6., No. 1 (2025)

  8.  Extending computational protein design to intrinsically disordered proteins.                                                                                                             P. Robustelli. https://www.science.org/doi/full/10.1126/sciadv.adr3239 (Invited Commentary)                                                                                Science Advances, 10, eadr3239  (2024)

  9. Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model.  T. Sisk & P. Robustelli, 
    https://www.pnas.org/doi/abs/10.1073/pnas.2313360121 ,                                                                                                                              Proceedings of the National Academy of Sciences, 121 (6), e2313360121  (2024)

  10. PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.                                      Ghafouri, H., Lazar, T., Del Conte, A., Ku, PED Consorium, P. Robustelli, L.G.T., Aspromonte, M., Bernadó, P., Chaves-Arquero, B., Chemes, L.B., Clementel, D., Cordeiro, T. and Elena-Real, C., 10.1093/nar/gkad947                                                                                                              Nucleic Acids Research, 2(D1), pp.D536-D544 (2024) 

  11. Rational optimization of a transcription factor activation domain inhibitor.                                                                                                               S. Basu, P. Martinez-Cristoabl, M. Pesarrodona, M. Frigole-Viva, E. Szulc, M. Lewis, A. Banuelos, C. Sanchexz-Zarzalego, S. Bielskute, J. Zhu, C. Garcia-Cabau, C. Batlee, B. Mateos, M. Biesaga, A. Escobedo, L. Bardia, X. Verdaguer, A. Ruffoni, N.R. Mawji, J. Wang, T. Tam, I. Brun-Heath, S. Ventura, D. Meierhofer, J. Garcia, P. Robustelli, T.H. Stracker, M.D. Sadar, A. Riera, D. Hnisz, X. Salvatella,  https://www.nature.com/articles/s41594-023-01159-5 ,                                                                                                                                       Nature Structural and Molecular Biology, 30 (12), 1958-1969 (2023) 

  12. Clustering heterogenous ensembles of intrinsically disordered proteins with t-distributed stochastic neighbour embedding,                          R. Appadurai, JK Koneru, M Bonomi, P. Robustelli, A. Srivastava, https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00224                                      Journal of Chemical Theory and Computation,  19, 14, 4711–4727 (2023) 

  13. Dissecting the biophysics and biology of intrinsically disordered proteins.                                                                                                             PR Banerjee,  AS Holehouse, R Kriwacki, P Robustelli, H Jiang, Al I Sobolevsky, J M. Hurley, JT Mendell       https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(23)00257-8 ,                                                                                     Trends in biochemical sciences, 49 (2), (2023)

  14. Small Molecules Targeting the Disordered Transactivation Domain of the Androgen Receptor Induce the Formation of Collapsed Helical States. J Zhu, X Salvatella, P Robustelli, https://www.nature.com/articles/s41467-022-34077-z ,                                                                       Nature Communications, 13 (1), 1-15  (2022) 

  15. Molecular basis of small-molecule binding to a-synuclein, P Robustelli, Ibanez-de-Opakua A, Campbell-Bezat C, Giordanetto F, Becker S, Zweckstette Mr, Pan AC, Shaw DE, https://pubs.acs.org/doi/full/10.1021/jacs.1c07591                                                                                    Journal of the American Chemical Society,144, 6, 2501–2510 (2022)                                                                                                                           

    Prior to Dartmouth:
     

  16. Quantifying the Relationship between Conformational Dynamics and Enzymatic Activity in Ribonuclease HI Homologues, J Martin, P Robustelli,  AG Palmer III, https://pubs.acs.org/doi/full/10.1021/acs.biochem.0c00500 ,  Biochemistry, 59 (35), 3201-3205 (2020)

  17. The Mechanism of Coupled Folding-Upon-Binding of An Intrinsically Disordered Protein, P Robustelli, S Piana, DE Shaw, Journal of the American Chemical Society (2020)

  18. Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. S Piana*, P Robustelli*, D Tan, S Chen, DE Shaw (*=equal contributions), Journal of Chemical Theory and Computation, 16, 4, 2494-2507 (2020)

  19. Developing a Molecular Dynamics Force Field for Both Folded and Disordered Protein States, P Robustelli, S Piana, DE Shaw, Proceedings of the National Academy of Sciences, p.201800690 (2018)

  20. Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States, S Piana, A Donchev, P Robustelli, DE Shaw, Journal of Physical Chemistry B, 119 (16), 5113-5123 (2015)

  21. Functional implications of large backbone amplitude motions of the glycoprotein 130-binding epitope of interleukin-6, R Bobby, P Robustelli, AV Kralicek, M Mobli, GF King, J Grötzinger, AJ Dingley, FEBS Journal, 281(10), 2471-83 (2014

  22. Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4, P Robustelli, N Trbovic, RA Friesner, AG Palmer III, Journal of Chemical Theory and Computation, 9(11), 5190–5200 (2013)

  23. Thermal Adaption of Conformational Dynamics in Ribonuclease H, KA Stafford, P Robustelli, AG Palmer III, PLoS Computational Biology, 9(10), e1003218 (2013)

  24. Structure of an Intermediate State in Protein Folding and Aggregation, P Neudecker, P Robustelli, A Cavalli, P Walsh, P Lundstrom, A Zarrine-Afsar, S Sharpe, M Vendruscolo, LE Kay, Science, 336, 362-366  (2012)

  25. Interpreting Protein Structural Dynamics from NMR Chemical Shifts, P Robustelli, KA Stafford, AG Palmer III, Journal of the American Chemical Society, 134, 6365-6374 (2012)

  26. Characterization of the Conformational Equilibrium Between the Two Major Substates of RNase A using NMR chemical shifts, C Camilloni, P Robustelli, A De Simone, A Cavalli, M Vendruscolo,  Journal of the American Chemical Society, 134, 3968-3971 (2012)

  27. Effects of the Known Pathogenic Mutations on the Aggregation Pathway of the Amyloidogenic Peptide of Apolipoprotein A-I, S Raimondi, F Guglielmi, S Giorgetti, S Di Gaetano, A Arciello, DM Monti, A Relini, D Nichino, SM Doglia, A Natalello, P Pucci, P Mangione, L Obici, G Merlini, M Stoppini, P Robustelli, GG Tartaglia, M Vendruscolo, CM Dobson, R Piccoli, V Bellotti, Journal of Molecular Biology, 407(3), 465-76 (2011)

  28. Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins, P Robustelli, KJ Kohlhoff, A Cavalli, M Vendrusculo, Structure, 18, 1-11 (2010)  

  29. Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distance, KJ Kohlhoff, P Robustelli, A Cavalli, X Salvatella, M Vendruscolo, Journal of the American Chemical Society, 131 (39), 13894-13895 (2009)

  30. Folding of Small Proteins with Chemical Shift Restrained Monte Carlo Simulations without the use of Molecular Fragment Replacement or Structural Homology, P Robustelli, A Cavalli, CM Dobson, M Vendruscolo, X Salvatella, Journal of Physical Chemistry B, 113 (22), 7890-7896 (2009)

  31. Determination of Protein Structures in the Solid State from NMR Chemical Shifts, P Robustelli, A Cavalli, M Vendruscolo, Structure, 16, 1764-1769 (2008)

  32. Structure and Conformational Dynamics of Tricothecene Mycotoxins, WE Steinmetz, P Robustelli, E Edens, D Heineman, Journal of Natural Products, 71 (4), 589-594 (2008) 

  33. A Molecular switch based on a biologically important redox reaction, P Yan, MW Holman, P Robustelli, A Chowdhury, FI Ishak, DM Adams, Journal of Physical Chemistry B, 109, 130-137 (2005)

All Rights Reserved by Robustelli Group

bottom of page