Now showing items 1-20 of 44

    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Ecoupling server: A tool to compute and analyze electronic couplings 

      Cabeza de Vaca, Israel; Acebes, Sandra; Guallar, Victor (Wiley Online Library, 2016-05-08)
      Article
      Open Access
      Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to ...
    • Enhancing backbone sampling in Monte Carlo simulations using Internal Coordinates Normal Mode Analysis 

      Gil, Victor A.; Lecina, Daniel; Grebner, Christoph; Guallar, Victor (Elsevier, 2016-07-04)
      Article
      Open Access
      Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application ...
    • Enrichment of virtual screening results using induced-fit techniques 

      Iglesias, Jelisa; Sae-oon, Suwipa; Hernandez, Gabriela; Estrada, Jorge; Gavaldà Mestre, Ricard; Guallar, Victor (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      This project aims to improve the results of virtual screening and docking techniques used for drug design, using induced-fit techniques and a consensus scoring approach.
    • Esterases computational study 

      Cañadas, Ruben; Santiago, Gerard; Guallar, Victor (Barcelona Supercomputing Center, 2017-05-04)
      Conference report
      Open Access
      In our project, we are focusing on two different esterases called LAE6 and LAE5. LAE6 is very promiscuous since it presents activity towards a wide range of different substrates, whereas LAE5 presents activity towards few ...
    • Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions 

      Grebner, Christoph; Lecina, Daniel; Gil, Victor; Ulander, Johan; Hansson, Pia; Dellsen, Anita; Tyrchan, Christian; Edman, Karl; Hogner, Anders; Guallar, Victor (Biophysical Society, 2017-03-28)
      Article
      Open Access
      In this study, we performed an extensive exploration of the ligand entry mechanism for members of the steroid nuclear hormone receptor family (androgen receptor, estrogen receptor α, glucocorticoid receptor, mineralocorticoid ...
    • FrAG-PELE: novel fragment-based growing tool for hit-to-lead in early drug discovery 

      Pérez López, Carles; Guallar, Victor (Barcelona Supercomputing Center, 2018-04-24)
      Conference report
      Open Access
    • Implementation of an internal coordinates anisotropic network model in PELE 

      Gil, Victor A.; Guallar, Victor (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      The use of computational methods to elucidate the ligand-protein binding mechanisms is of utmost importance for the pharmaceutical industry. PELE (Protein Energy Landscape Exploration) software has proved to have ...
    • Inhibition of Human Enhancer of Zeste Homolog 2 (EZH2) with Tambjamine Analogs 

      Kotev, Martin; Manuel-Manresa, Pilar; Hernando, Elsa; Soto-Cerrato, Vanessa; Orozco, Modesto; Quesada, Roberto; Pérez-Tomás, Ricardo; Guallar, Victor (American Chemical Society, 2017-08-01)
      Article
      Open Access
      Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This ...
    • Interactive GPU-based generation of solvent-excluded surfaces 

      Hermosilla, Pedro; Krone, Michael; Guallar, Victor; Vázquez, Pere-Pau; Vinacua Pla, Álvaro; Ropinski, Timo (Springer International Publishing, 2017-06)
      Article
      Open Access
      The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific ...
    • Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases 

      Acebes, Sandra; Ruiz-Dueñas, Francisco J.; Toubes, Mario; Sáez-Jiménez, Veronica; Pérez-Boada, Marta; Lucas, M. Fatima; Martínez, Angel T.; Guallar, Victor (ACS Publications, 2017-04-04)
      Article
      Open Access
      Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role ...