Google scholar links here.


  • JG Glanzer, KA Carnes, P Soto, S Liu, LJ Parkhurst, GG Oakley. A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A Nucleic Acids Research.
  • M Grabenauer, C Wu, P Soto, JE Shea, MT. Bowers. Oligomers of the prion protein fragment 106-126 are likely assembled from beta-hairpins in solution, and methionine oxidation inhibits assembly without altering the peptide's monomeric conformation. J Am Chem Soc. 2010, 132(2):532-539.
  • BD Armstrong, P Soto, P.; J.-E. Shea, S. Han. Overhauser dynamic nuclear polarization and molecular dynamics simulations using pyrroline and piperidine ring nitroxide radicals. J. Magn. Reson. 2009, 200, 137-141
  • Z Zhuang, AI Jewett, P Soto, JE Shea. Effect of surface tethering on the folding of the src-SH3 protein domain. Phys. Biol. 2009, 6, 015004.
  • MG Krone, L Hua, P Soto, R. Zhou, BJ Berne, JE Shea. Role of Water in Mediating the Assembly of Alzheimer Amyloid-b Ab16−22 Protofilaments. Journal of the American Chemical Society 2008, 30(33): 11066-11072.
  • G Colombo, P Soto and E Gazit. Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology. Trends in Biotechnology 2007, 25:211-218.
  • P Soto, MA Griffin, JE Shea. New insights into the mechanism of Alzheimer amyloid-b fibrillogenesis inhibition by N-methyl peptides.  Biophysical Journal 2007, 93(9): 3015-3025.
  • P Soto, A Baumketner, JE Shea. Aggregation of polyalanine in a hydrophobic environment. Journal of Chemical Physics 2006, 124:134904.
  • P Soto, R Zangi. Characterization of the stereochemical selectivity of b-hairpin formation by molecular dynamics simulations Journal of Physical Chemistry B. 2005, 109 (3): 1281-1288.
  • P Soto, J Cladera, AE Mark, X Daura. Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations Angewandte Chemie-International Edition 2005, 44 (7): 1065-1067.
  • P Soto, G Colombo. Characterization of the conformational space of a triple-stranded b-sheet forming peptide with molecular dynamics simulations Proteins: Structure, Function, and Bioinformatics 2004, 57: 734-746.
  • P Soto, AE Mark. The effect of the neglect of electronic polarization in peptide folding simulations Journal of Physical Chemistry B 2002, 106: 12830-12833.
In Spanish:
  •  P Soto, F Espejo, LM Salazar, R Fayad. Simulación computacional del comportamiento de un péptido sintético Revista Colombiana de Física 1999, 31: 151-154 (title in English: Computational  simulation of a synthetic peptide).
  •   P Soto, G Cavelier. Estructura y simulación del canal iónico de melitina Revista Colombiana de Fisica 1997, 29: 407-410 (title in English: Structure and simulation of the melittin ion channel).

Non-peer reviewed:

  • P Soto. Aplicación de las simulaciones de dinámica molecular al estudio del comportamiento de biomoléculas en solución Bioquímica PUCV 2004, 10: 10-13 (title in English: Computational simulations to study the behavior of biomolecules in solution).
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