Electronic and Atomic Protein Modeling (EAPM)

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Showing 91 - 120 results of 173

2015

Basidiomycete DyPs: Genomic diversity, structural‚Äìfunctional aspects, reaction mechanism and environmental significance

Archives of Biochemistry and Biophysics

D. Linde, F. J. Ruiz-Dueñas, E. Fernández-Fueyo, V. Guallar, K. E. Hammel, R. Pogni, and A. T. Mart√≠nez
Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase

FEBS Journal

P. Ferreira, A. Hernández-Ortega, F. Lucas, J. Carro, B. Herguedas, K. W. Borrelli, V. Guallar, A. T. Martínez, and M. Medina

2014

Computation and experiment meet together: a powerful approach to rational re-design of oxidoreductases

OxiZymes2014. Vienna, Austria

E. Monza
Binding free energy and ligand orientation calculations using Monte Carlo method with Markov State analysis

Entropy in Biomolecular Systems Workshop. Vienna, Austria

D. Lecina
Coupling Protein Dynamics with Active Site Chemistry: a MM and QM tale

ICPP8 International Conference on Porphyrins and Phtalocyanines, Istanbul, Turkey
Using PELE for Structural Biology

4th Visegrad Symposium on Structural Systems Biology, Nove Hrady, Czech Republic

V. Guallar
Correlated Inter-Domain Motions in Adenylate Kinase

PLoS computational biology

S. Esteban-Martín, R. Bryn Fenwick, J. \ AAdén, B. Cossins, C. W. Bertoncini, V. Guallar, M. Wolf-Watz, and X. Salvatella
Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi

Acta Crystallographica Section D: Biological Crystallography

E. Fernández-Fueyo, S. Acebes, F. J. Ruiz-Dueñas, M. Jesús Martínez, A. Romero, F. Javier Medrano, V. Guallar, and A. T. Martínez
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
Conformational Response to Ligand Binding in Phosphomannomutase2 INSIGHTS INTO INBORN GLYCOSYLATION DISORDER

Journal of Biological Chemistry

G. Andreotti, I. Cabeza de Vaca, A. Poziello, M. Chiara Monti, V. Guallar, and M. Vittoria Cubellis
Atomic Level Rendering of DNA-Drug Encounter

Biophysical Journal

M. F. Lucas, I. Cabeza de Vaca, R. Takahashi, J. Rubio-Martinez, and V. Guallar
Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations

Journal of Chemical Theory and Computation

R. Takahashi, V. A. Gil, and V. Guallar
Atomic Picture of Ligand Migration in Toluene 4-Monooxygenase

The Journal of Physical Chemistry B

A. Hosseini, M. Brouk, M F. Lucas, F. Glaser, A. Fishman, and V. Guallar
Differential Control of Heme Reactivity in Alpha and Beta Subunits of Hemoglobin: A Combined Raman Spectroscopic and Computational Study

Journal of the American Chemical Society

E. M. Jones, E. Monza, G. Balakrishnan, G. C. Blouin, P. J. Mak, Q. Zhu, J. R. Kincaid, V. Guallar, and T. G. Spiro
pyProCT: Automated Cluster Analysis for Structural Bioinformatics

Journal of Chemical Theory and Computation

V. AlejandroGil, and V. Guallar

2013

Monte Carlo Free Ligand Diffusion and Absolute Binding Free Energy Calculations

Molecular Kinetic 2013. Berlin, Germany

R. Takahashi
Mapping Complex Electron transfer in Proteins by Computational Tools

34 Reunión Bienal de la RSEQ, Santander, Spain

V. Guallar
QM and MM methods: Obtaining an electronic and atomic view of nature

Biology centre of the Academy of Sciences, Czech Republic

V. Guallar
QM and MM methods: Obtaining an electronic and atomic view of nature

2nd Synthetic Biology Minisymposium, National University of Singapore, Singapor

V. Guallar
Mapping Complex Electron transfer in Proteins by Computational Tools

V. Guallar
QM and MM methods: Obtaining an electronic and atomic view of nature

2nd Congress of Computational Biology and Bioinformatics, Manizales, Colombia

V. Guallar
pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

Bioinformatics (Oxford, England)

V. A. Gil, and V. Guallar
Electron transfer in proteins: theory, applications and future perspectives.

Physical chemistry chemical physics : PCCP

S. Saen-oon, M F. Lucas, and V. Guallar
In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c.

PLoS computational biology

F. H. Wallrapp, A. A. Voityuk, and V. Guallar
Single vs. multiple ligand pathways in globins: A computational view.

Biochimica et biophysica acta

F. M. Lucas, and V. Guallar
Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism.

The Biochemical journal

Y. Miki, R. Pogni, S. Acebes, F. Lucas, E. Fernández-Fueyo, M C. Baratto, M. I. Fernández, V. de Los Ríos, F. J. Ruiz-Dueñas, A. Sinicropi, R. Basosi, K. E. Hammel, V. Guallar, and A. T. Martínez
Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2.

Biochimica et biophysica acta

F. Spyrakis, F. Lucas, A. Bidon-Chanal, C. Viappiani, V. Guallar, and J. F. Luque
Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.

PloS one

J. J. Valdés, A. Schwarz, I. Cabeza de Vaca, E. Calvo, J. H. F. Pedra, V. Guallar, and M. Kotsyfakis
PELE web server: atomistic study of biomolecular systems at your fingertips.

Nucleic acids research

A. Madadkar-Sobhani, and V. Guallar
Molecular Interactions of Prodiginines with the BH3 Domain of Anti-Apoptotic Bcl-2 Family Members.

PloS one

A. Hosseini, M. Espona-Fiedler, V. Soto-Cerrato, R. Quesada, R. Pérez-Tomás, and V. Guallar

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