Electronic and Atomic Protein Modeling (EAPM)

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Showing 61 - 90 results of 173

2017

Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions

Biophysical Journal

C. Grebner, D. Lecina, V. Gil, J. Ulander, P. Hansson, A. Dellsen, C. Tyrchan, K. Edman, A. Hogner, and V. Guallar

2016

Re-designing the substrate binding pocket of laccase for enhanced oxidation of sinapic acid

Catalysis Science & Technology

I.. Pardo, L. Santus, P.. Gentili, F.. Lucas, E.. Monza, F.. J. Medrano, C.. Galli, A.. T. Martínez, V. Guallar, and S.. Camarero
Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

Catalysis Science & Technology

D. Linde, M. Cañellas, C. Coscolín, I. Davó-Siguero, A. Romero, F. Lucas, F. J. Ruiz-Dueas, V. Guallar, and A. T. Martínez
The unravelling of the complex pattern of tyrosinase inhibition

Scientific Reports

B. Deri, M. Kanteev, M. Goldfeder, D. Lecina, V. Guallar, N. Adir, and A. Fishman
Computational Prediction of HIV-1 Resistance to Protease Inhibitors

Journal of Chemical Information and Modeling

A. Hosseini, A. Alibés, M. Noguera-Julian, V. Gil, R. Paredes, R. Soliva, M. Orozco, and V. Guallar
Active-Site-Directed Inhibitors of Prolyl Oligopeptidase Abolish Its Conformational Dynamics

ChemBioChem

A. López, F. Herranz-Trillo, M. Kotev, M. Gairí, V. Guallar, P. Bernadó, O. Millet, T. Tarragó, and E. Giralt
Unveiling the basis of alkaline stability of an evolved versatile peroxidase

Biochemical Journal

V.. Saez-Jimenez, S. Acebes, E.. Garcia-Ruiz, A.. Romero, V. Guallar, M.. Alcalde, F.. J. Medrano, A.. T. Martínez, and F.. J. Ruiz-Duenas
Ecoupling server: A tool to compute and analyze electronic couplings

Journal of Computational Chemistry

I. Cabezade Vaca, S. Acebes, and V. Guallar
Computer-Aided Laccase Engineering: Toward Biological Oxidation of Arylamines

ACS Catalysis

G. Santiago, F. de Salas, F. M. Lucas, E. Monza, S. Acebes, A. T. Martínez, S. Camarero, and V. Guallar
Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis

Bioorganic & Medicinal Chemistry

V. A. Gil, D. Lecina, C. Grebner, and V. Guallar
Rational Enzyme Engineering Through Biophysical and Biochemical Modeling

ACS Catalysis

S. Acebes, E. Fernández-Fueyo, E. Monza, F. M. Lucas, D. Almendral, F. J. Ruiz-Dueñas, H. Lund, A. T. Martínez, and V. Guallar
Synthesis of 1-Naphthol by a Natural Peroxygenase engineered by Directed Evolution

ChemBioChem

P. Molina-Espeja, M. Cañellas, F. J. Plou, M. Hofrichter, F. Lucas, V. Guallar, and M. Alcalde
Molecular determinants for selective C25-hydroxylation of vitamins D2 and D3 by fungal peroxygenases

Catalysis Science & Technology

F. Lucas, E. D. Babot, M. Cañellas, J. C. del Rio, L. Kalum, R. Ullrich, M. Hofrichter, V. Guallar, A. T. Martínez, and A. Gutiérrez
Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

IEEE Transactions on Visualization and Computer Graphics

R.. Skanberg, P.-P.. Vazquez, V. Guallar, and T.. Ropinski
High quality illustrative effects for molecular rendering

Computers & Graphics

P. Hermosilla, V. Guallar, A.. Vinacua, and P.P.. Vázquez

2015

Interactive Drug Design with Monte Carlo Simulations

4th JLESC Workshop

J. Estrada
Mapping biophysics through enhanced Monte Carlo techniques

I. Cabeza de Vaca
Instant Visualization of Secondary Structures of Molecular Models

Eurographics Workshop on Visual Computing for Biology and Medicine

P. Hermosilla, V. Guallar, A. Vinacua, and P-P. Vázquez
Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy

Journal of Physical Chemistry Letters

E. Monza, F. M. Lucas, S. Camarero, L. C. Alejaldre, A. T. Martínez, and V. Guallar
Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding

Journal of Physical Chemistry B

M. I. Giannotti, I. Cabeza de Vaca, J. M. Artés, F. Sanz, V. Guallar, and P. Gorostiza
Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor

ChemMedChem

N. Bayó-Puxan, R. Rodríguez-Mias, M. Goldflam, M. Kotev, S. Ciudad, C. J. Hipolito, M. Varese, H. Suga, R. Campos-Olivas, X. Barril, V. Guallar, M. Teixidó, J. García, and E. Giralt
New Monte Carlo Based Technique To Study DNA–Ligand Interactions

Journal of Chemical Theory and Computation

I. Cabeza de Vaca, M F. Lucas, and V. Guallar
Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway

The Journal of Biological Chemistry

J. Kopečná, I. Cabeza de Vaca, N. B. P. Adams, P. A. Davison, A. A. Brindley, N. C. Hunter, V. Guallar, and R. Sobotka
Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints

Structure

K. Edman, A. Hosseini, M. K. Bjursell, A. Aagaard, L. Wissler, A. Gunnarsson, T. Kaminski, C. Köhler, S. Bäckström, T. J. Jensen, A. Cavallin, U. Karlsson, E. Nilsson, D. Lecina, R. Takahashi, C. Grebner, S. Geschwindner, M. Lepistö, A. C. Hogner, and V. Guallar
A theoretical multiscale treatment of protein–protein electron transfer: The ferredoxin/ferredoxin-NADP+ reductase and flavodoxin/ferredoxin-NADP+ reductase systems

Biochimica et Biophysica Acta (BBA) - Bioenergetics

S. Saen-oon, I. Cabeza de Vaca, D. Masone, M. Medina, and V. Guallar
Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

Biochemical Journal

L. Dolores, P. Rebecca, C. Marina, L. Fatima, G. Victor, C. Baratto Maria, S. Adalgisa, S-jimenez. Veronica, C. Cristina, R. Antonio, and
Improving the Oxidative Stability of a High Redox Potential Fungal Peroxidase by Rational Design

PLOs One

V. Sáez-Jiménez, S. Acebes, V. Guallar, A. T. Martínez, and F. J. Ruiz-Dueñas
Steroid hydroxylation by basidiomycete peroxygenases: A combined experimental and computational study

Applied and environmental microbiology

E. D. Babot, C. José, M. Cañellas, F. Sancho, F. Lucas, V. Guallar, L. Kalum, H. Lund, G. Gröbe, K. Scheibner, and
Modeling protein dynamics and protein-drug interactions with Monte Carlo based techniques

Universitat de Barcelona

A. Hosseini
Unveiling Prolyl Oligopeptidase Ligand Migration by Comprehensive Computational Techniques

Biophysical journal

M. Kotev, D. Lecina, T. Tarragó, E. Giralt, and V. Guallar

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