Now showing items 1-20 of 81

    • A platform for antibody design 

      Díaz Rovira, Anna Maria; Guallar, Victor (Barcelona Supercomputing Center, 2022-05)
      Conference report
      Open Access
      Antibodies are specialized proteins produced by our adaptive immune system to identify and neutralize specific molecules (antigens) of foreign objects, such as pathogenic microorganisms or infected cells. Due to their ...
    • A theoretical multiscale treatment of protein-protein electron transfer: the ferredoxin/ferredoxin-NADP+ reductase and flavodoxin/ferredoxin-NADP+ reductase systems 

      Saen-oon, Suwipa; Cabeza de Vaca, Israel; Medina, Milagros; Guallar, Victor (Elsevier, 2015-12)
      Article
      Open Access
      In the photosynthetic electron transfer (ET) chain, two electrons transfer from photosystem I to the flavin- dependent ferredoxin-NADP+ reductase (FNR) via two sequential independent ferredoxin (Fd) electron carriers. In ...
    • Accelerating binding free energy calculations by combining Monte Carlo simulations, enhanced sampling and Markov State Models 

      Gilabert, Joan F.; Guallar, Victor (Barcelona Supercomputing Center, 2018-04-24)
      Conference report
      Open Access
    • Active-Site-Directed Inhibitors of Prolyl Oligopeptidase Abolish Its Conformational Dynamics 

      López, Abraham; Herranz-Trillo, Fátima; Kotev, Martin; Gairí, Margarida; Guallar, Victor; Bernadó, Pau; Millet, Oscar; Tarragó, Teresa; Giralt, Ernest (Wiley, 2016-05-17)
      Article
      Open Access
      Deciphering conformational dynamics is crucial for understanding the biological functions of proteins and for designing compounds targeting them. In particular, providing an accurate description of microsecond–millisecond ...
    • Adaptive simulations, towards interactive protein-ligand modeling 

      Lecina, Daniel; Gilabert, Joan F.; Guallar, Victor (2017-08-16)
      Article
      Open Access
      Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few ...
    • AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design 

      Roda, Sergi; Terholsen, Henrik; Heike Meyer, Jule Ruth; Cañellas Solé, Albert; Guallar, Victor; Bornscheuer, Uwe; Kazemi, Masoud (American Chemical Society, 2023)
      Article
      Open Access
      With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light of these advances, structure-based enzyme engineering is expected to become increasingly ...
    • Binding free energy and ligand orientation calculations using a Monte Carlo method with Markov Sate analysis 

      Lecina-Casas, Daniel; Takahashi, Ryoji; Guallar, Victor (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      Computing binding free energies has great implications in drug design. Using PELE technique, it has been shown that one can get quick and accurate estimations by means of a Markov state model3. We improved our methodology ...
    • Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils 

      Peccati, Francesca; Pantaleone, Stefano; Riffet, Vanessa; Solans-Monfort, Xavier; Contreras-García, Julia; Guallar, Victor; Sodupe, Mariona (American Chemical Society, 2017-08-29)
      Article
      Open Access
      Alzheimer’s disease is a challenge of the utmost importance for contemporary society. An early diagnosis is essential for the development of treatments and for establishing a network of support for the patient. In this ...
    • Chronological brain lesions after SARS-CoV-2 infection in hACE2-transgenic mice 

      Vidal, Enric; López Figueroa, Carlos; Rodon, Jordi; Pérez, Mónica; Brustolin, Marco; Guallar, Victor (SAGE Publications, 2021-12)
      Article
      Open Access
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes respiratory disease, but it can also affect other organs including the central nervous system. Several animal models have been developed to address different ...
    • Clinical course impacts early kinetics,magnitude, and amplitude of SARS-CoV-2 neutralizing antibodies beyond 1 year after infection 

      Pradenas, Edwards; Trinité, Benjamin; Urrea, Víctor; Marfil, Silvia; Tarrés Freixas, Ferran; Guallar, Victor; Valencia, Alfonso (Cell Press, 2022-02)
      Article
      Open Access
      To understand the determinants of long-term immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the concurrent impact of vaccination and emerging variants, we follow a prospective cohort ...
    • Combining Monte Carlo and molecular dynamics simulations for enhanced binding free energy estimation through Markov State models 

      Gilabert, Joan F.; Gracia Carmona, Oriol; Hogner, Anders; Guallar, Victor (American Chemical Society, 2020)
      Article
      Open Access
      We present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one of the most significant challenges in computer-aided drug design. The ...
    • Comprehensive insights into the production of long chain aliphatic aldehydes using a copper-radical alcohol oxidase as biocatalyst 

      Ribeaucourt, David; Bissaro, Bastien; Guallar, Victor; Yemloul, Mehdi; Haon, Mireille; Grisel, Sacha; Alphand, Véronique; Brumer, Harry; Lambert, Fanny; Berrin, Jean-Guy; Lafond, Mickael (American Chemical Society, 2021)
      Article
      Open Access
      The oxidation of alcohols is a cornerstone reaction in chemistry, notably in the flavor and fragrance industry where long-chain aliphatic aldehydes are major odorant compounds. In a context where greener alternatives are ...
    • Computational structure‐based drug design: Predicting target flexibility 

      Iglesias Fernández, Jelisa Maria; Saen-oon, Suwipa; Soliva Soliva, Robert; Guallar, Victor (Wiley, 2018-04-29)
      Article
      Open Access
      The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing ...
    • Computationally driven rational design of substrate promiscuity on serine ester hydrolases 

      Roda, Sergi; Fernandez Lopez, Laura; Cañadas, Rubén; Santiago, Gerard; Ferrer, Manuel; Guallar, Victor (American Chemical Society, 2021)
      Article
      Open Access
      Enzymes with a broad substrate specificity are of great interest both at the basic and applied level. Understanding the main parameters that make an enzyme substrate ambiguous could be thus important not only for their ...
    • De novo binding prediction of peptides to MHC class I 

      Gracia, Oriol; Amengual-Rigo, Pep; Guallar, Victor (Barcelona Supercomputing Center, 2019-05-07)
      Conference report
      Open Access
    • Description of a Non-Canonical Mn(II)-Oxidation Site in Peroxidases 

      Fernández-Fueyo, Elena; Davó-Siguero, Irene; Almendral, David; Linde, Dolores; Baratto, Maria C.; Pogni, Rebecca; Romero, Antonio; Guallar, Victor; Martinez, Angel T. (American Chemical Society, 2018-07-31)
      Article
      Open Access
      A dye-decolorizing peroxidase (DyP) from Pleurotus ostreatus (PosDyP4) catalyzes the oxidation of Mn2+ to Mn3+, in the presence of H2O2, with an efficiency similar to the well-known manganese peroxidases and versatile ...
    • Design and characterization of in-one protease-esterase pluriZyme 

      Fernandez Lopez, Laura; Roda, Sergi; Gonzalez Alfonso, Jose L.; Plou, Francisco J.; Guallar, Victor; Ferrer, Manuel (MDPI, 2022)
      Article
      Open Access
      Proteases are abundant in prokaryotic genomes (~10 per genome), but their recovery encounters expression problems, as only 1% can be produced at high levels; this value differs from that of similarly abundant esterases ...
    • Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain 

      Segalés, Joaquim; Puig, Mariona; Rodon, Jordi; Avila-Nieto, Carlos; Carrillo, Jorge; Cantero, Guillermo; Terrón, Maria Teresa; Cruz, Sílvia; Parera, Mariona; Noguera-Julián, Marc; Izquierdo-Useros, Nuria; Guallar, Victor; Vidal, Enric; Valencia, Alfonso; Blanco, Ignacio; Blanco, Julià; Clotet, Bonaventura; Vergara-Alert, Júlia (National Academy of Sciences, 2020-10)
      Article
      Open Access
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is considered a zoonotic pathogen mainly transmitted human to human. Few reports indicate that pets may be exposed to the ...
    • Development of corrections for the absolute free binding energy prediction 

      Puch-Giner, Ignasi; Municoy Terol, Martí; Guallar, Victor (Barcelona Supercomputing Center, 2022-05)
      Conference report
      Open Access
      The early stages of drug design rely on hit discovery programs, where initial possible inhibitors’ binding affinities are assessed when bound to their biological target. It is an expensive and time-consuming process, ...
    • Discovery and biochemical characterization of thermostable glycerol oxidases 

      Santema, Lars L.; Rotilio, Laura; Xiang, Ruite; Tjallinks, Gwen; Guallar, Victor; Mattevi, Andrea; Fraaije, Marco W. (Springer, 2024)
      Article
      Open Access
      Alditol oxidases are promising tools for the biocatalytic oxidation of glycerol to more valuable chemicals. By integrating in silico bioprospecting with cell-free protein synthesis and activity screening, an effective ...