Publications

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2015
P. Ferreira, Hernández-Ortega, A., Lucas, F., Carro, J., Herguedas, B., Borrelli, K. W., Guallar, V., Martínez, A. T., and Medina, M., Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase, FEBS Journal. p. n/a–n/a, 2015.
D. Linde, Ruiz-Dueñas, F. J., Fernández-Fueyo, E., Guallar, V., Hammel, K. E., Pogni, R., and Mart√≠nez, A. T., Basidiomycete DyPs: Genomic diversity, structural‚Äìfunctional aspects, reaction mechanism and environmental significance, Archives of Biochemistry and Biophysics. p. -, 2015.
D. Linde, Ruiz-Dueñas, F. J., Fernández-Fueyo, E., Guallar, V., Hammel, K. E., Pogni, R., and Mart√≠nez, A. T., Basidiomycete DyPs: Genomic diversity, structural‚Äìfunctional aspects, reaction mechanism and environmental significance, Archives of Biochemistry and Biophysics. p. -, 2015.
N. Bayó-Puxan, Rodríguez-Mias, R., Goldflam, M., Kotev, M., Ciudad, S., Hipolito, C. J., Varese, M., Suga, H., Campos-Olivas, R., Barril, X., Guallar, V., Teixidó, M., García, J., and Giralt, E., Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor, ChemMedChem. WILEY-VCH Verlag, p. n/a–n/a, 2015.
M. I. Giannotti, Cabeza de Vaca, I., Artés, J. M., Sanz, F., Guallar, V., and Gorostiza, P., Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding, The Journal of Physical Chemistry B, vol. 119. pp. 12050-12058, 2015.
V. Sáez-Jiménez, Acebes, S., Guallar, V., Martínez, A. T., and Ruiz-Dueñas, F. J., Improving the Oxidative Stability of a High Redox Potential Fungal Peroxidase by Rational Design, POs One, vol. 10, no. 4. p. e0124750, 2015.
E. Monza, M. Lucas, F., Camarero, S., Alejaldre, L. C., Martínez, A. T., and Guallar, V., Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy, The Journal of Physical Chemistry Letters, vol. 6. American Chemical Society, pp. 1447-1453, 2015.
K. Edman, Hosseini, A., Bjursell, M. K., Aagaard, A., Wissler, L., Gunnarsson, A., Kaminski, T., Köhler, C., Bäckström, S., Jensen, T. J., Cavallin, A., Karlsson, U., Nilsson, E., Lecina, D., Takahashi, R., Grebner, C., Geschwindner, S., Lepistö, M., Hogner, A. C., and Guallar, V., Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints, Structure, vol. 23. pp. 2280 - 2290, 2015.
I. Cabeza de Vaca, Lucas, M. F., and Guallar, V., New Monte Carlo Based Technique To Study DNA–Ligand Interactions, Journal of Chemical Theory and Computation, vol. 11. pp. 5598-5605, 2015.
J. Kopečná, de Vaca, I. Cabeza, Adams, N. B. P., Davison, P. A., Brindley, A. A., C. Hunter, N., Guallar, V., and Sobotka, R., Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway, Journal of Biological Chemistry, vol. 290. pp. 28477-28488, 2015.
E. D. Babot, José, C., Cañellas, M., Sancho, F., Lucas, F., Guallar, V., Kalum, L., Lund, H., Gröbe, G., Scheibner, K., and , Steroid hydroxylation by basidiomycete peroxygenases: A combined experimental and computational study, Applied and environmental microbiology, vol. 81. American Society for Microbiology, pp. 4130–4142, 2015.
P. Molina-Espeja, Cañellas, M., Plou, F. J., Hofrichter, M., Lucas, F., Guallar, V., and Alcalde, M., Synthesis of 1-Naphthol by a Natural Peroxygenase engineered by Directed Evolution, ChemBioChem. p. n/a–n/a, 2015.
S. Saen-oon, Cabeza de Vaca, I., Masone, D., Medina, M., and Guallar, V., 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, vol. 1847. pp. 1530 - 1538, 2015.
M. Kotev, Lecina, D., Tarragó, T., Giralt, E., and Guallar, V., Unveiling Prolyl Oligopeptidase Ligand Migration by Comprehensive Computational Techniques, Biophysical journal, vol. 108. Cell Press, pp. 116–125, 2015.
2014
M. F. Lucas, de Vaca, I. Cabeza, Takahashi, R., Rubio-Martinez, J., and Guallar, V., Atomic Level Rendering of DNA-Drug Encounter, Biophysical Journal, vol. 106. pp. 421 - 429, 2014.
A. Hosseini, Brouk, M., Lucas, M. F., Glaser, F., Fishman, A., and Guallar, V., Atomic Picture of Ligand Migration in Toluene 4-Monooxygenase, The Journal of Physical Chemistry B. p. null, 2014.
D. Lecina, Binding free energy and ligand orientation calculations using Monte Carlo method with Markov State analysis, Entropy in Biomolecular Systems Workshop. Vienna, Austria . 2014.
E. Monza, Computation and experiment meet together: a powerful approach to rational re-design of oxidoreductases, OxiZymes2014. Vienna, Austria . 2014.
G. Andreotti, de Vaca, I. Cabeza, Poziello, A., Monti, M. Chiara, Guallar, V., and Cubellis, M. Vittoria, Conformational Response to Ligand Binding in Phosphomannomutase2 INSIGHTS INTO INBORN GLYCOSYLATION DISORDER, Journal of Biological Chemistry, vol. 289. American Society for Biochemistry and Molecular Biology, pp. 34900–34910, 2014.
S. Esteban-Martín, Fenwick, R. Bryn, AAdén, J. \, Cossins, B., Bertoncini, C. W., Guallar, V., Wolf-Watz, M., and Salvatella, X., Correlated Inter-Domain Motions in Adenylate Kinase, PLoS computational biology, vol. 10. Public Library of Science, p. e1003721, 2014.
V. Guallar, Coupling Protein Dynamics with Active Site Chemistry: a MM and QM tale, ICPP8 International Conference on Porphyrins and Phtalocyanines, Istanbul, Turkey. 2014.
E. M. Jones, Monza, E., Balakrishnan, G., Blouin, G. C., Mak, P. J., Zhu, Q., Kincaid, J. R., Guallar, V., and Spiro, T. G., 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. p. null, 2014.
R. Takahashi, Gil, V. A., and Guallar, V., Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations, Journal of Chemical Theory and Computation, vol. 10. pp. 282-288, 2014.
V. Alejandro Gil and Guallar, V., pyProCT: Automated Cluster Analysis for Structural Bioinformatics, Journal of Chemical Theory and Computation. p. null, 2014.
E. Fernández-Fueyo, Acebes, S., Ruiz-Dueñas, F. J., Martínez, M. Jesús, Romero, A., Medrano, F. Javier, Guallar, V., and Martínez, A. T., 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, vol. 70. International Union of Crystallography, pp. 0–0, 2014.
V. Guallar, Using PELE for Structural Biology, 4th Visegrad Symposium on Structural Systems Biology, Nove Hrady, Czech Republic . 2014.
2013
F. Spyrakis, Lucas, F., Bidon-Chanal, A., Viappiani, C., Guallar, V., and Luque, J. F., Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2., Biochimica et biophysica acta. 2013.
S. Rao, Raj, S., Cossins, B., Marro, M., Guallar, V., and Petrov, D., Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering., Biophysical journal, vol. 104, no. 1. pp. 156-62, 2013.
S. Saen-oon, Lucas, M. F., and Guallar, V., Electron transfer in proteins: theory, applications and future perspectives., Physical chemistry chemical physics : PCCP, vol. 15, no. 37. pp. 15271-85, 2013.
Y. Miki, Pogni, R., Acebes, S., Lucas, F., Fernández-Fueyo, E., Baratto, M. C., Fernández, M. I., de Los Ríos, V., Ruiz-Dueñas, F. J., Sinicropi, A., Basosi, R., Hammel, K. E., Guallar, V., and Martínez, A. T., Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism., The Biochemical journal, vol. 452, no. 3. pp. 575-84, 2013.
F. H. Wallrapp, Voityuk, A. A., and Guallar, V., In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c., PLoS computational biology, vol. 9, no. 3. p. e1002990, 2013.
V. Guallar, Mapping Complex Electron transfer in Proteins by Computational Tools. Real Sociedad Española de Quimica, Santander, 2013.
V. Guallar, Mapping Complex Electron transfer in Proteins by Computational Tools, 34 Reunión Bienal de la RSEQ, Santander, Spain . 2013.
A. Hosseini, Espona-Fiedler, M., Soto-Cerrato, V., Quesada, R., Pérez-Tomás, R., and Guallar, V., Molecular Interactions of Prodiginines with the BH3 Domain of Anti-Apoptotic Bcl-2 Family Members., PloS one, vol. 8, no. 2. p. e57562, 2013.
R. Takahashi, Monte Carlo Free Ligand Diffusion and Absolute Binding Free Energy Calculations, Molecular Kinetic 2013. Berlin, Germany. 2013.
A. Madadkar-Sobhani and Guallar, V., PELE web server: atomistic study of biomolecular systems at your fingertips., Nucleic acids research, vol. 41, no. Web Server issue. pp. W322-8, 2013.
V. A. Gil and Guallar, V., pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling., Bioinformatics (Oxford, England), vol. 29, no. 18. pp. 2363-4, 2013.
V. Guallar, QM and MM methods: Obtaining an electronic and atomic view of nature, 2nd Congress of Computational Biology and Bioinformatics, Manizales, Colombia. 2nd Congress of Computational Biology and Bioinformatics, Manizales, Colombia, 2013.
V. Guallar, QM and MM methods: Obtaining an electronic and atomic view of nature. 2nd Synthetic Biology Minisymposium, National University of Singapore, Singapore, 2013.
V. Guallar, QM and MM methods: Obtaining an electronic and atomic view of nature , Biology centre of the Academy of Sciences, Czech Republic. 2013.
V. Guallar, QM and MM methods: Obtaining an electronic and atomic view of nature, 2nd Synthetic Biology Minisymposium, National University of Singapore, Singapor. 2nd Synthetic Biology Minisymposium, Singapore , 2013.
F. M. Lucas and Guallar, V., Single vs. multiple ligand pathways in globins: A computational view., Biochimica et biophysica acta. 2013.
F. M. Lucas and Guallar, V., Single vs. multiple ligand pathways in globins: A computational view., Biochimica et biophysica acta. 2013.
J. J. Valdés, Schwarz, A., Cabeza de Vaca, I., Calvo, E., Pedra, J. H. F., Guallar, V., and Kotsyfakis, M., Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder., PloS one, vol. 8, no. 5. p. e62562, 2013.

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