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S. J. Fleishman, Whitehead, T. A., Strauch, E. - M., Corn, J. E., Qin, S., Zhou, H. - X., Mitchell, J. C., Demerdash, O. N. A., Takeda-Shitaka, M., Terashi, G., Moal, I. H., Li, X., Bates, P. A., Zacharias, M., Park, H., Ko, J. -su, Lee, H., Seok, C., Bourquard, T., Bernauer, J., Poupon, A., Azé, J., Soner, S., Ovali, S. K., Ozbek, P., Tal, N. B., Haliloglu, T., Hwang, H., Vreven, T., Pierce, B. G., Weng, Z., Pérez-Cano, L., Pons, C., Fernández-Recio, J., Jiang, F., Yang, F., Gong, X., Cao, L., Xu, X., Liu, B., Wang, P., Li, C., Wang, C., Robert, C. H., Guharoy, M., Liu, S., Huang, Y., Li, L., Guo, D., Chen, Y., Xiao, Y., London, N., Itzhaki, Z., Schueler-Furman, O., Inbar, Y., Potapov, V., Cohen, M., Schreiber, G., Tsuchiya, Y., Kanamori, E., Standley, D. M., Nakamura, H., Kinoshita, K., Driggers, C. M., Hall, R. G., Morgan, J. L., Hsu, V. L., Zhan, J., Yang, Y., Zhou, Y., Kastritis, P. L., Bonvin, A. M. J. J., Zhang, W., Camacho, C. J., Kilambi, K. P., Sircar, A., Gray, J. J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, Y., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodríguez, J., Kihara, D., Stranges, B. P., Jacak, R., Kuhlman, B., Huang, S. - Y., Zou, X., Wodak, S. J., Janin, J., and Baker, D., Community-wide assessment of protein-interface modeling suggests improvements to design methodology., Journal of molecular biology, vol. 414, no. 2. pp. 289-302, 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.
L. Helft, Reddy, V., Chen, X., Koller, T., Federici, L., Fernández-Recio, J., Gupta, R., and Bent, A., LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains., PloS one, vol. 6, no. 7. p. e21614, 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.
L. Kowalczyk, Ratera, M., Paladino, A., Bartoccioni, P., Errasti-Murugarren, E., Valencia, E., Portella, G., Bial, S., Zorzano, A., Fita, I., Orozco, M., Carpena, X., Vázquez-Ibar, J. L., and Palacín, M., Molecular basis of substrate-induced permeation by an amino acid antiporter., Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 10. pp. 3935-40, 2011.
A. N. Naganathan and Orozco, M., The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding., Journal of the American Chemical Society, vol. 133, no. 31. pp. 12154-61, 2011.
C. Pons, Glaser, F., and Fernández-Recio, J., Prediction of protein-binding areas by small-world residue networks and application to docking., BMC bioinformatics, vol. 12. p. 378, 2011.
A. N. Naganathan and Orozco, M., The protein folding transition-state ensemble from a Gō-like model., Physical chemistry chemical physics : PCCP, vol. 13, no. 33. pp. 15166-74, 2011.
C. Pons, Talavera, D., de la Cruz, X., Orozco, M., and Fernández-Recio, J., Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking., Journal of chemical information and modeling, vol. 51, no. 2. pp. 370-7, 2011.
S. Ayuso-Tejedor, García-Fandiño, R., Orozco, M., Sancho, J., and Bernadó, P., Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Journal of molecular biology, vol. 406, no. 4. pp. 604-19, 2011.
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.
V. Guallar, Baik, M. - H., Lippard, S. J., and Friesner, R. A., Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450., Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 12. pp. 6998-7002, 2003.