Modeling of processes with peptides and proteins


  • Blanco, P.M.; Madurga, S.; Garces, J.L.; Mas, F.; Dias, Rita S.  Influence of macromolecular crowding on the charge regulation of intrinsically disordered proteins. Soft Matter, 17, 2021, 655-669.
  • Barazorda-Ccahuana,; Nedyalkova, M.; Mas, F.; Madurga, S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers, 13, 2021, 3823.
  • Nedyalkova, M.; Vasighi, M.; Sappati, S.; Kumar, A.; Madurga, S.; Simeonov, V.  Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach. Pharmaceuticals, 14, 2021, 1328.


  • Barazorda-Ccahuana, H.L.; Gomez, B.; Mas, F.; Madurga, S.    Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations. Polymers, 12, 2020, 2713.
  • Naneva, L.; Nedyalkova, M.; Madurga, S.; Mas, F.; Simeonov, V. Applying Discriminant and Cluster Analyses to Separate Allergenic from Non-allergenic Proteins. Open Chemistry, 17, 2019, 401-407.
  • Dimova, D.; Pisov, S.; Panchev, N.; Nedyalkova, M.; Madurga, S.; Proykova, A.  Insight into electric field-induced rupture mechanism of water-in-toluene emulsion films from a model system. Journal Of Chemical Physics, 146, 2017, 194703.  
  • López, A.; Vilaseca, M.; Madurga, S.; Varese, M.; Tarragó, T.; Giralt, E. 2016.Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyloligopeptidase, Journal of Mass Spectrometry, 51(7), 504-511. doi:


  • Martín-Quirós, M.; Nevola, L.; Eckelt, K.; Madurga, S.; Gorostiza, P.; Giralt, E. 2015.Absence of a stable secondary structure is not a limitation for photoswitchable inhibitors of beta-arrestin/beta-adaptin 2 protein-protein interaction, Chemistry & Biology, 22(1), 31-37. doi:
  • Escribano, E.; Madurga, S.; Vilaseca, M.; Moreno, V. 2014. Ion mobility and Top-down MS complementary approaches for the structural analysis of protein models bound to anticancer metallodrugs, Inorganica Chimica Acta, 423, 60-69. doi:
  • Serra-Vidal, B.; Pujadas, L.; Rossi, D.; Soriano, D.; Madurga, S.; Carulla, N. 2014.Hydrogen/Deuterium Exchange-Protected Oligomers Populated during A2 Fibril Formation Correlate with Neuronal Cell Death, ACS Chemica Biology, 9(11), 2678-2685. doi:
  • Sánchez, L.; Madurga, S.; Pukala, T.; Vilaseca, M.; López-Iglesias, C.; Robinson, C.V.; Giralt, E.; Carulla, N. 2011. A240 and A242 Amyloid Fibrils Exhibit Distinct Molecular Recycling Properties, Journal of the American Chemical Society, 133(17), 6505-6508. doi:


  • Llop-Tous, I.; S. Madurga; E. Giralt; P. Marzabal; M. Torrent; M.D. Ludevid. 2010. Relevant elements of a proline-rich tag involved in protein body biogenesis in nicotiana benthamiana, Journal of Biological Chemistry, en prensa.
  • Tarragó, T.; J. Martín-Benito; E. Sabidó; B. Claasen; S. Madurga; M. Gairí; J.M. Valpuesta; E. Giralt. 2009. A new side opening on prolyl oligopeptidase revealed by electron microscopy, Febs Letters, 583:3344-3348.
  • Grillo-Bosch, D.; N. Carulla; M. Cruz; L. Sanchez; R. Pujol-Pina; S. Madurga; F. Rabanal; E. Giralt. 2009. Retro-enantio N-methylated peptides as beta-amyloid aggregation inhibitors. ChemMedChem 4:1488-1494.
  • Gaston, F.; G.C. Granados; S. Madurga; F. Rabanal; F. Lakhdar-Ghazal; E. Giralt; E. Bahraoui. 2009. Development and characterization of peptidic fusion inhibitors derived from HIV-1 gp41 with partial D-amino acid substitutions. ChemMedChem 4:570-581.
  • Villacañas, O.; S. Madurga; E. Giralt; I. Belda. 2009. Explicit treatment of water molecules in protein-ligand docking. Current Computer-Aided Drug Design. 5:145-154.
  • Fàbrega, A.; S. Madurga; E. Giralt; J. Vila. 2009. Mechanism of action of and resistance to quinolone. Microbial Biotechnology, 2:40-61.
  • Madurga, S.; J. Sánchez-Céspedes; I. Belda; J. Vila; E. Giralt. 2008. Mechanism of Binding of Fluoroquinolones to the Quinolone Resistance-Determining Region of DNA Gyrase: Towards an Understanding of the Molecular Basis of Quinolone Resistance. Chembiochem. 9:2081-2086.
  • Belda, I.; S. Madurga; T. Tarragó; X. Llorà and E. Giralt. 2007. Evolutionary computation and multimodal search: A good combination to tackle molecular diversity in the field of peptide design. Molecular Diversity, 11:7-21.
  • Frutos, S.; R.A. Rodriguez-Mias; S. Madurga; B. Collinet; M. Reboud-Ravaux; D. Ludevid; E. Giralt. 2007. Disruption of the HIV-1 protease dimer with interface peptides: Structural studies using NMR spectroscopy combined with [2-C-13]-Trp selective labeling. Biopolymers, 88:164-173.
  • Gairí, M.; P. Saiz; S. Madurga; X. Roig; J. Erchegyi; S.C. Koerber; J.C. Reubi; J.E. Rivier; E. Giralt. 2006. Conformational analysis of a potent SSTR3-selective somatostatin analogue by NMR in water solution. Journal of Peptide Science, 12:82-91.
  • Madurga, S.; I. Belda; X. Llora; E. Giralt. 2005. Design of enhanced agonists through the use of a new virtual screening method: Application to peptides that bind class I major histocompatibility complex (MHC) molecules. Protein Science, 14:2069-2079.
  • Belda, I.; S. Madurga; X. Llora; M. Martinell; T. Tarrago; M.G. Piqueras; E. Nicolas; E. Giralt. 2005. ENPDA: an evolutionary structure-based de novo peptide design algorithm. Journal of Computer-Aided Molecular Design, 19:585-601.