Now showing items 1-20 of 41

  • 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 ...
  • 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 ...
  • 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, Jelisa; Saen-oon, Suwipa; 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 ...
  • 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, Carlos; 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 ...
  • Modulating Fatty Acid Epoxidation vs Hydroxylation in a Fungal Peroxygenase 

    Carro, Juan; González-Benjumea, Alejandro; Fernández-Fueyo, Elena; Aranda, Carmen; Guallar, Victor; Gutiérrez, Ana; Martínez, Angel T. (American Chemical Society, 2019-06-14)
    Article
    Open Access
    Unspecific peroxygenases (UPOs) are fungal secreted counterparts of the cytochrome P450 monooxygenases present in most living cells. Both enzyme types share the ability to perform selective oxygenation reactions. Moreover, ...