Browsing by Author "Guallar, Víctor"
Now showing items 1-20 of 26
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Adaptive on-the-fly molecular ribbons generation
(European Association for Computer Graphics (Eurographics), 2015)
Conference lecture
Open AccessMolecular 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
(FEBSPress, 2015-02-23)
Article
Open AccessAryl-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
(Royal Society of Chemistry, 2016-05-23)
Article
Open AccessThe 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
(ACS Publications, 2014-05-04)
Article
Open AccessComputational 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
(Elsevier, 2015-05-15)
Article
Open AccessThe 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
(Portland Press, 2015-03-01)
Article
Open AccessDye-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
(Wiley Online Library, 2015-11-10)
Article
Open AccessThe 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
(American Chemical Society, 2016-04-15)
Article
Open AccessDevelopment 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
(ACS Publications, 2015-09-10)
Article
Open AccessThe 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 ... -
FragPELE: dynamic ligand growing within a binding site. A novel tool for hit-to-lead drug design
(American Chemical Society (ACS), 2020)
Article
Open AccessThe early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, ... -
High quality illustrative effects for molecular rendering
(2016-02)
Article
Restricted access - publisher's policyAll-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
(PLoS, 2015-04-29)
Article
Open AccessLigninolytic 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
(ACS Publications, 2015-03-30)
Article
Open AccessUnderstanding 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
(European Association for Computer Graphics (Eurographics), 2015)
Conference report
Open AccessMolecular 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
(Springer, 2017-05-08)
Article
Open AccessThe 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
(Elsevier, 2015-12-01)
Article
Open AccessSteroid 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
(Royal Society of Chemistry, 2015-08-07)
Article
Open AccessHydroxylation 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
(ACS Publications, 2015-11-03)
Article
Open AccessWe 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
(2017-01-01)
Article
Open AccessMolecular 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
(American Society for Biochemistry and Molecular Biology, 2015-10-07)
Article
Open AccessIn 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 ...
