Publications

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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.
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. íctorA., 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.
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.
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. 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.
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.
2012
F. M. Lucas and Guallar, V., An atomistic view on human hemoglobin carbon monoxide migration processes., Biophysical journal, vol. 102, no. 4. pp. 887-96, 2012.
F. M. Lucas, Cisplatin, still a long way to go, TACC-2012, Theory and Applications in Computational Chemistry. Pavia, Lombardia, Italy. 2012.
B. P. Cossins, Hosseini, A., and Guallar, V., Exploration of Protein Conformational Change with PELE and Meta-Dynamics, Journal of Chemical Theory and Computation, vol. 8. pp. 959-965, 2012.
D. Masone, Cabeza de Vaca, I., Pons, C., Fernández-Recio, J., and Guallar, V., H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?, Proteins, vol. 80, no. 3. pp. 818-24, 2012.
M. Espona-Fiedler, Soto-Cerrato, V., Hosseini, A., Lizcano, J. M., Guallar, V., Quesada, R., Gao, T., and Pérez-Tomás, R., Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: Prodigiosin vs. obatoclax., Biochemical pharmacology, vol. 83, no. 4. pp. 489-96, 2012.
V. Guallar, PELE: Low Cost Protein-Ligand Dynamics and Induced Fit, Structural & Computational Chemistry, Discovery Congress Chemistry, Munich (Germany) . 2012.
A. Hernández-Ortega, Lucas, F., Ferreira, P., Medina, M., Guallar, V., and Martínez, A. T., Role of active site histidines in the two half-reactions of the aryl-alcohol oxidase catalytic cycle., Biochemistry, vol. 51, no. 33. pp. 6595-608, 2012.
A. Hernández-Ortega, Ferreira, P., Merino, P., Medina, M., Guallar, V., and Martínez, A. T., Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily., Chembiochem : a European journal of chemical biology. 2012.
M. A. Yu, Egawa, T., Shinzawa-Itoh, K., Yoshikawa, S., Guallar, V., Yeh, S. - R., Rousseau, D. L., and Gerfen, G. J., Two tyrosyl radicals stabilize high oxidation States in cytochrome C oxidase for efficient energy conservation and proton translocation., Journal of the American Chemical Society, vol. 134, no. 10. pp. 4753-61, 2012.
F. Lucas, Masone, D., Saen-oon, S., Wallrapp, F., and Guallar, V., Using QM/MM Methods for the Exploration of Electron Transfer Pathways, Current Inorganic Chemistry, vol. 2, no. 3. pp. 263-272 , 2012.
2011
F. M. Lucas, Rousseau, D. L., and Guallar, V., Electron transfer pathways in cytochrome c oxidase., Biochimica et biophysica acta, vol. 1807, no. 10. pp. 1305-13, 2011.
D. Masone, Cabeza de Vaca, I., Pons, C., Recio, J. F., and Guallar, V., H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?, Proteins. 2011.
A. Hernández-Ortega, Lucas, F., Ferreira, P., Medina, M., Guallar, V., and Martínez, A. T., Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine., The Journal of biological chemistry, vol. 286, no. 47. pp. 41105-14, 2011.
B. P. Cossins, Jacobson, M. P., and Guallar, V., A new view of the bacterial cytosol environment., PLoS computational biology, vol. 7, no. 6. p. e1002066, 2011.
V. Daskalakis, Farantos, S. C., Guallar, V., and Varotsis, C., Regulation of electron and proton transfer by the protein matrix of cytochrome c oxidase., The journal of physical chemistry. B, vol. 115, no. 13. pp. 3648-55, 2011.
A. Hernández-Ortega, Borrelli, K., Ferreira, P., Medina, M., Martínez, A. T., and Guallar, V., Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase., The Biochemical journal, vol. 436, no. 2. pp. 341-50, 2011.
2008
F. Wallrapp, Masone, D., and Guallar, V., Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway., The journal of physical chemistry. A, vol. 112, no. 50. pp. 12989-94, 2008.
V. Guallar, Heme electron transfer in peroxidases: the propionate e-pathway., The journal of physical chemistry. B, vol. 112, no. 42. pp. 13460-4, 2008.
V. Guallar and Wallrapp, F., Mapping protein electron transfer pathways with QM/MM methods., Journal of the Royal Society, Interface / the Royal Society, vol. 5 Suppl 3. pp. S233-9, 2008.
M. A. Martí, Bidon-Chanal, A., Crespo, A., Yeh, S. - R., Guallar, V., Luque, F. J., and Estrin, D. A., Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N., Journal of the American Chemical Society, vol. 130, no. 5. pp. 1688-93, 2008.
Q. Wang, Xia, J., Guallar, V., Krilov, G., and Kantrowitz, E. R., Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases., Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 44. pp. 16918-23, 2008.
M. A. Marti, Capece, L., Bidon-Chanal, A., Crespo, A., Guallar, V., Luque, F. J., and Estrin, D. A., Nitric oxide reactivity with globins as investigated through computer simulation., Methods in enzymology, vol. 437. pp. 477-98, 2008.

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