Now showing items 21-40 of 41

  • Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution 

    Monza, Emanuele; Acebes, Sandra; Lucas, Fátima; Guallar, Victor (Springer, 2017-02-15)
    Part of book or chapter of book
    Open Access
    Directed evolution (DE) creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding, and catalysis. Although this technique does not require any structural/mechanistic ...
  • Monte Carlo Techniques for Drug Design: The Success Case of PELE 

    Gilabert, Joan F.; Lecina, Daniel; Estrada, Jorge; Guallar, Victor (Wiley, 2018-12-21)
    Part of book or chapter of book
    Open Access
    This chapter summarizes the most representative software packages that readily allow running Monte Carlo (MC) simulations in relevant scenarios for drug design. It explores in detail the Protein Energy Landscape Exploration ...
  • Multiple implications of an active site phenylalanine in the catalysis of aryl-alcohol oxidase 

    Carro, Juan; Amengual-Rigo, Pep; Sancho, Ferran; Medina, Milagros; Guallar, Victor; Ferreira, Patricia; Martinez, Angel T. (Nature Publishing Group, 2018-05-25)
    Article
    Open Access
    Aryl-alcohol oxidase (AAO) has demonstrated to be an enzyme with a bright future ahead due to its biotechnological potential in deracemisation of chiral compounds, production of bioplastic precursors and other reactions ...
  • On the way to real time protein-ligand sampling 

    Lecina-Casas, Daniel; Takahashi, Ryoji; Guallar, Victor (Barcelona Supercomputing Center, 2015-05-05)
    Conference report
    Open Access
    Protein-ligand binding free energy is one of the keystones of drug design, and developing a fast method to calculate it would have great impact in personalized medicine. However, it is a daunting task for computational ...
  • Oxidoreductases on their way to industrial biotransformations 

    Martinez, Angel T.; Ruiz-Dueñas, Francisco; Camarero, Susana; Serrano, Ana; Linde, Dolores; Lund, Henrik; Vind, Jesper; Tovborg, Morten; Herold-Majumdar, Owik M.; Hofrichter, Martin; Liers, Christiane; Ullrich, René; Scheibner, Katrin; Sannia, Giovanni; Piscitelli, Alessandra; Pezzella, Cinzia; Sener, Mehmet E.; Kiliç, Sibel; van Berkel, Willhem J.H.; Guallar, Victor; Lucas, Fátima; Zuhse, Ralf; Ludwig, Roland; Hollmann, Frank; Fernández-Fueyo, Elena; Record, Eric; Faulds, Craig B.; Tortajada, Marta; Winckelmann, Ib; Rasmussen, Jo-Anne; Gelo-Pujic, Mirjana; Gutiérrez, Ana; del Río, José C.; Rencoret, Jorge; Alcalde, Miguel (Elsevier, 2017-11)
    Article
    Open Access
    Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant ...
  • Physics-Based Visual Characterization of Molecular Interaction Forces 

    Hermosilla, Pedro; Estrada, Jorge; Guallar, Victor; Ropinski, Timo; Vinacua, Álvar; Vázquez, Pere-Pau (IEEE, 2017-01)
    Article
    Open Access
    Molecular design procedures, such as drug design and protein engineering’ are complex processes, largely benefiting from computational resources but also from human analysis. In drug design, for example, a costly iterative ...
  • PluriZymes: new enzymes for new times 

    Domingo-Cabasés, Marc; Rodà, Sergi; Santiago, Gerard; Guallar, Victor (Barcelona Supercomputing Center, 2019-05-07)
    Conference report
    Open Access
  • Probing the Surface of a Laccase for Clues towards the Design of Chemo-Enzymatic Catalysts 

    Robert, Viviane; Monza, Emanuele; Tarrago, Lionel; Sancho, Ferran; de Falco, Ana; Schneider, Ludovic; Ngoutane, Eloïne N.; Mekmouche, Yasmina; Pailley, Pierre R.; Simaan, A. Jalila; Guallar, Victor; Tron, Thierry (Wiley, 2017-04)
    Article
    Open Access
    Systems featuring a multi-copper oxidase associated with transition-metal complexes can be used to perform oxidation reactions in mild conditions. Here, a strategy is presented for achieving a controlled orientation of a ...
  • Protein modelling for enzyme engineering 

    Santiago, Gerard; Guallar, Victor (Barcelona Supercomputing Center, 2017-05-04)
    Conference report
    Open Access
  • Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case 

    Kotev, Martin; Pascual, Rosalia; Almansa, Carmen; Guallar, Victor; Soliva, Robert (American Chemical Society, 2018-07-27)
    Article
    Open Access
    Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. ...
  • Rational Engineering of Multiple Active Sites in an Ester Hydrolase 

    Santiago, Gerard; Martínez-Martínez, Mónica; Alonso, Sandra; Bargiela, Rafael; Coscolín, Cristina; Golyshing, Peter N.; Guallar, Victor; Ferrer, Manuel (American Chemical Society, 2018-03-30)
    Article
    Open Access
    Effects of altering the properties of an active site in an enzymatic homogeneous catalyst have been extensively reported. However, the possibility of increasing the number of such sites, as commonly done in heterogeneous ...
  • Real-time molecular visualization supporting diffuse interreflections and ambient occlusion 

    Skanberg, Robin; Vázquez Alcocer, Pere Pau; Guallar, Victor; Ropinski, Timo (2016-01-01)
    Article
    Open Access
    Today molecular simulations produce complex data sets capturing the interactions of molecules in detail. Due to the complexity of this time-varying data, advanced visualization techniques are required to support its visual ...
  • Repurposing designed mutants: a valuable strategy for computer-aided laccase engineering – the case of POXA1b 

    Giacobelli, Valerio G.; Monza, Emanuele; Lucas, M. Fatima; Pezzella, Cinzia; Piscitelli, Alessandra; Guallar, Victor; Sannia, Giovanni (Royal Society of Chemistry, 2017-01-04)
    Article
    Open Access
    The broad specificity of laccases, a direct consequence of their shallow binding site, makes this class of enzymes a suitable template to build specificity toward putative substrates. In this work, a computational methodology ...
  • Sampling interfacial water effects over protein specificity with PELE 

    Guallar, Victor; Municoy, Martí; Carrillo Parramon, Oliver (Barcelona Supercomputing Center, 2018-04-24)
    Conference report
    Open Access
  • Selective synthesis of 4-hydroxyisophorone and 4-ketoisophorone by fungal peroxygenases 

    Aranda, Carmen; Municoy, Martí; Guallar, Victor; Kiebist, Jan; Scheibner, Katrin; Ullrich, René; del Río, José C.; Hofrichter, Martin; Martinez, Angel T.; Gutierrez, Ana (Royal Society of Chemistry, 2019-02-26)
    Article
    Open Access
    The recently discovered unspecific peroxygenases (UPOs) from the ascomycetes Chaetomium globosum and Humicola insolens were capable of selectively hydroxylating isophorone to 4-hydroxyisophorone (4HIP) and 4-ketoisophorone ...
  • Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design 

    Lucas, M. Fatima; Monza, Emanuele; Jorgensen, Lise J.; Ernst, Heidi A.; Piontek, Klaus; Bjerrum, Morten J.; Martinez, Angel T.; Camarero, Susana; Guallar, Victor (2017-02-10)
    Article
    Open Access
    To meet the very specific requirements demanded by industry, proteins must be appropriately tailored. Engineering laccases, to improve the oxidation of small molecules, with applications in multiple fields, is, however, a ...
  • Switching the substrate preference of fungal aryl-alcohol oxidase: towards stereoselective oxidation of secondary benzyl alcohols 

    Serrano, Ana; Sancho, Ferran; Viña-González, Javier; Carro, Juan; Alcalde, Miguel; Guallar, Victor; Martínez, Angel T. (Royal Society of Chemistry, 2019-01-22)
    Article
    Open Access
    Oxidation of primary alcohols by aryl-alcohol oxidase (AAO), a flavoenzyme that provides H2O2 to fungal peroxidases for lignin degradation in nature, is achieved by concerted hydroxyl proton transfer and stereoselective ...
  • Synthesis of 1‐Naphthol by a Natural Peroxygenase engineered by Directed Evolution 

    Molina-Espeja, Patricia; Cañellas, Marina; Plou, Francisco J.; Hofrichter, Martin; Lucas, Fatima; Guallar, Victor; Alcalde, Miguel (Wiley-VCH, 2016-01-21)
    Article
    Open Access
    There is an increasing interest in enzymes that catalyze the hydroxylation of naphthalene under mild conditions and with minimal requirements. To address this challenge, an extracellular fungal aromatic peroxygenase with ...
  • The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths 

    Gygli, Gudrun; Lucas, Maria F.; Guallar, Victor; van Berkel, Willhem J.H. (Public Library of Science, 2017-10-06)
    Article
    Open Access
    Vanillyl alcohol oxidase (VAO) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family. Each VAO subunit consists of two domains, the FAD-binding and the cap domain. VAO catalyses, among other reactions, the ...
  • The unravelling of the complex pattern of tyrosinase inhibition 

    Deri, Batel; Kanteev, Margarita; Goldfeder, Mor; Lecina, Daniel; Guallar, Victor; Adir, Noam; Fishman, Ayelet (Nature Publishing Group, 2016-10-11)
    Article
    Open Access
    Tyrosinases are responsible for melanin formation in all life domains. Tyrosinase inhibitors are used for the prevention of severe skin diseases, in skin-whitening creams and to avoid fruit browning, however continued use ...