Now showing items 1-20 of 24

  • Adaptive on-the-fly molecular ribbons generation 

    Hermosilla, Pedro; Guallar, Víctor; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (European Association for Computer Graphics (Eurographics), 2015)
    Conference lecture
    Open Access
    Molecular dynamics simulations are of key importance in the drug design field. One common used representation to visualize these simulations is the Ribbons representation, which gives to the expert a good overview of the ...
  • Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase 

    Ferreira, Patricia; Hernández-Ortega, Aitor; Lucas, Fatima; Carro, Juan; Herguedas, Beatriz; Borrelli, Kenneth W.; Guallar, Víctor; Martínez, Angel T.; Medina, Milagros (FEBSPress, 2015-02-23)
    Article
    Open Access
    Aryl-alcohol oxidase (AAO, EC 1.1.3.7) generates H2O2 for lignin degradation at the expense of benzylic and other π system-containing primary alcohols, which are oxidized to the corresponding aldehydes. Ligand diffusion ...
  • Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase 

    Linde, Dolores; Cañellas, Marina; Coscolín, Cristina; Davó-Siguero, Irene; Romero, Antonio; Lucas, Fátima; Ruiz-Dueñas, Francisco J.; Guallar, Víctor; Martínez, Ángel T. (Royal Society of Chemistry, 2016-05-23)
    Article
    Open Access
    The so-called dye-decolorizing peroxidases (DyPs) constitute a new family of proteins exhibiting remarkable stability. With the aim of providing them new catalytic activities of biotechnological interest, the heme pocket ...
  • Atomic picture of ligand migration in toluene 4-monooxygenase 

    Hosseini, Ali; Brouk, Moran; Lucas, Fatima; Glaser, Fabian; Fishman, Ayelet; Guallar, Víctor (ACS Publications, 2014-05-04)
    Article
    Open Access
    Computational modeling combined with mutational and activity assays was used to underline the substrate migration pathways in toluene 4-monooxygenase, a member of the important family of bacterial multicomponent monooxygenases ...
  • Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance 

    Linde, Dolores; Ruiz-Dueñas, Francisco J.; Fernandez-Fueyo, Elena; Guallar, Víctor; Hammel, Kenneth E.; Pogni, Rebecca; Martínez, Angel T. (Elsevier, 2015-05-15)
    Article
    Open Access
    The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, ...
  • Catalytic surface radical in dye-decolorizing peroxidase: A computational, spectroscopic and directed mutagenesis study 

    Linde, Dolores; Pogni, Rebecca; Cañellas, Marina; Lucas, Fátima; Guallar, Víctor; Ruiz-Dueñas, Francisco J.; Baratto, Maria Camilla; Sinocro, Adalgisa; Coscolin, Cristina; Romero, Antonio; Medrano, Francisco Javier; Martínez, Angel T. (Portland Press, 2015-03-01)
    Article
    Open Access
    Dye-decolorizing peroxidase (DyP) of Auricularia auriculajudae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational ...
  • Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor 

    Bayó-Puxan, Núria; Rodríguez-Mias, Ricard; Goldflam, Michael; Kotev, Martin; Ciudad, Sonia; Hipolito, Christopher J.; Varese, Monica; Suga, Hiroaki; Campos-Olivas, Ramón; Barril, Xavier; Guallar, Víctor; Teixidó, Meritxell; García, Jesús; Giralt, Ernest (Wiley Online Library, 2015-11-10)
    Article
    Open Access
    The modulation of protein–protein interactions (PPIs) is emerging as a highly promising tool to fight diseases. However, whereas an increasing number of compounds are able to disrupt peptide-mediated PPIs efficiently, the ...
  • Computational Prediction of HIV-1 Resistance to Protease Inhibitors 

    Hosseini, Ali; Alibés, Andreu; Noguera-Julian, Marc; Gil, Victor; Paredes, Roger; Soliva, Robert; Orozco, Modesto; Guallar, Víctor (American Chemical Society, 2016-04-15)
    Article
    Open Access
    Development of mutations in HIV-1 PR hinders the activity of antiretroviral drugs, forcing changes in drug prescription. Most resistance assessments used to date rely on expert-based rules on predefined sets of stereotypical ...
  • Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding 

    Giannotti, Marina; Cabeza de Vaca, Israel; Artés, Juan M.; Sanz, Fausto; Guallar, Víctor; Gorostiza, Pau (ACS Publications, 2015-09-10)
    Article
    Open Access
    The structural basis of the low reorganization energy of cupredoxins has long been debated. These proteins reconcile a conformationally heterogeneous and exposed metal-chelating site with the highly rigid copper center ...
  • High quality illustrative effects for molecular rendering 

    Hermosilla Casajús, Pedro; Guallar, Víctor; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (2016-02)
    Article
    Restricted access - publisher's policy
    All-atom simulations are crucial in biotechnology. In Pharmacology, for example, molecular knowledge of protein-drug interactions is essential in the understanding of certain pathologies and in the development of improved ...
  • Improving the Oxidative Stability of a High Redox Potential Fungal Peroxidase by Rational Design 

    Sáez-Jiménez, Veronica; Acebes, Sandra; Guallar, Víctor; Martínez, Angel T.; Ruiz-Dueñas, Francisco Javier (PLoS, 2015-04-29)
    Article
    Open Access
    Ligninolytic peroxidases are enzymes of biotechnological interest due to their ability to oxidize high redox potential aromatic compounds, including the recalcitrant lignin polymer. However, different obstacles prevent ...
  • Insights on Laccase Engineering from Molecular Simulations: Towards a Binding Focused Strategy 

    Monza, Emanuele; Lucas, Fatima; Camarero, Susana; Alejaldre, Lorea C.; Martínez, Angel T.; Guallar, Víctor (ACS Publications, 2015-03-30)
    Article
    Open Access
    Understanding the molecular determinants of enzyme performance is of primary importance for the rational design of ad hoc mutants. A novel approach, which combines efficient conformational sampling and quick reactivity ...
  • Instant visualization of secondary structures of molecular models 

    Hermosilla, Pedro; Guallar, Víctor; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (European Association for Computer Graphics (Eurographics), 2015)
    Conference report
    Open Access
    Molecular Dynamics simulations are of key importance in the drug design field. Among all possible representations commonly used to inspect these simulations, Ribbons has the advantage of giving the expert a good overview ...
  • Interactive GPU-based generation of solvent-excluded surfaces 

    Hermosilla Casajús, Pedro; Krone, Michael; Guallar, Víctor; Vázquez Alcocer, Pere Pau; Vinacua Pla, Álvaro; Ropinski, Timo (Springer, 2017-05-08)
    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 ...
  • Ligand binding mechanism in steroid receptors; from conserved plasticity to differential evolutionary constraints 

    Edman, Karl; Hosseini, Ali; Bjursell, Magnus K.; Aagaard, Anna; Wissler, Lisa; Gunnarsson, Anders; Kaminski, Tim; Köhler, Christian; Bäckström, Stefan; Jensen, Tina J.; Cavallin, Anders; Karlsson, Ulla; Nilsson, Ewa; Lecina, Daniel; Takahashi, Ryoji; Grebner, Christoph; Geschwindner, Stefan; Lepistö, Matti; Hogner, Anders C.; Guallar, Víctor (Elsevier, 2015-12-01)
    Article
    Open Access
    Steroid receptor drugs have been available for more than half a century, but details 24 of the ligand binding mechanism has remained elusive. We solved X-ray structures of 25 the glucocorticoid and mineralocorticoid receptors ...
  • Molecular determinants for selective C 25-hydroxylation of vitamins D 2 and D 3 by fungal peroxygenases 

    Lucas, Fátima; Babot, Esteban D.; Cañellas, Marina; del Río, José C.; Kalum, Lisbeth; Ullrich, René; Hofrichter, Martin; Guallar, Víctor; Martínez, Ángel T.; Gutiérrez, Ana (Royal Society of Chemistry, 2015-08-07)
    Article
    Open Access
    Hydroxylation of vitamin D by Agrocybe aegerita and Coprinopsis cinerea peroxygenases was investigated in a combined experimental and computational study. 25-Monohydroxylated vitamin D3 (cholecalciferol) and D2 (ergocalciferol), ...
  • New Monte Carlo Based Technique To Study DNA–Ligand Interactions 

    Cabeza de Vaca, Israel; Lucas, Fatima; Guallar, Víctor (ACS Publications, 2015-11-03)
    Article
    Open Access
    We present a new all-atom Monte Carlo technique capable of performing quick and accurate DNA–ligand conformational sampling. In particular, and using the PELE software as a frame, we have introduced an additional force ...
  • Physics-based visual characterization of molecular interaction forces 

    Hermosilla, Pedro; Estrada, Jorge; Guallar, Víctor; Ropinski, Timo; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (2017-01-01)
    Article
    Open Access
    Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major ...
  • Porphyrin Binding to Gun4 protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway 

    Kopečná, Jana; Cabeza de Vaca, Israel; Ademas, Nathan B. P.; Davison, Paul A.; Brindley, Amanda A.; Hunter, C. Neil; Guallar, Víctor; Sobotka, Roman (American Society for Biochemistry and Molecular Biology, 2015-10-07)
    Article
    Open Access
    In oxygenic phototrophs, chlorophylls, hemes and bilins are synthesized by a common branched pathway. Given the phototoxic nature of tetrapyrroles, this pathway must be tightly regulated and an important regulatory role ...
  • Rational Enzyme Engineering Through Biophysical and Biochemical Modeling 

    Acebes, Sandra; Fernández-Fueyo, Elena; Monza, Emanuele; Lucas, Fatima; Almendral, David; Ruiz-Dueñas, Fracisco J.; Lund, Henrik; Martínez, Ángel T.; Guallar, Víctor (ACS Publications, 2016-02-03)
    Article
    Open Access
    Due to its importance in the pharmaceutical industry, ligand dynamic simulations have experienced a great expansion. Using all-atom models and cutting edge hardware, one can perform non-biased ligand migration, active site ...