Publications

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2011
Fleishman, S.J., 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. & Baker, D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of molecular biology 414, 289-302 (2011).
Lucas, F.M., Rousseau, D.L. & Guallar, V. Electron transfer pathways in cytochrome c oxidase. Biochimica et biophysica acta 1807, 1305-13 (2011).
Helft, L., Reddy, V., Chen, X., Koller, T., Federici, L., Fernández-Recio, J., Gupta, R. & Bent, A. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. PloS one 6, e21614 (2011).
Hernández-Ortega, A., Lucas, F., Ferreira, P., Medina, M., Guallar, V. & 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 286, 41105-14 (2011).
Kowalczyk, L., 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. & 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 108, 3935-40 (2011).
Naganathan, A.N. & Orozco, M. The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. Journal of the American Chemical Society 133, 12154-61 (2011).
Pons, C., Glaser, F. & Fernández-Recio, J. Prediction of protein-binding areas by small-world residue networks and application to docking. BMC bioinformatics 12, 378 (2011).
Naganathan, A.N. & Orozco, M. The protein folding transition-state ensemble from a Gō-like model. Physical chemistry chemical physics : PCCP 13, 15166-74 (2011).
Pons, C., Talavera, D., de la Cruz, X., Orozco, M. & 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 51, 370-7 (2011).
Ayuso-Tejedor, S., García-Fandiño, R., Orozco, M., Sancho, J. & Bernadó, P. Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering. Journal of molecular biology 406, 604-19 (2011).
2008
Wallrapp, F., Masone, D. & Guallar, V. Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway. The journal of physical chemistry. A 112, 12989-94 (2008).
Guallar, V. Heme electron transfer in peroxidases: the propionate e-pathway. The journal of physical chemistry. B 112, 13460-4 (2008).
Guallar, V. & Wallrapp, F. Mapping protein electron transfer pathways with QM/MM methods. Journal of the Royal Society, Interface / the Royal Society 5 Suppl 3, S233-9 (2008).
Martí, M.A., Bidon-Chanal, A., Crespo, A., Yeh, S.-R., Guallar, V., Luque, F.J. & Estrin, D.A. Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N. Journal of the American Chemical Society 130, 1688-93 (2008).
Wang, Q., Xia, J., Guallar, V., Krilov, G. & 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 105, 16918-23 (2008).
Marti, M.A., Capece, L., Bidon-Chanal, A., Crespo, A., Guallar, V., Luque, F.J. & Estrin, D.A. Nitric oxide reactivity with globins as investigated through computer simulation. Methods in enzymology 437, 477-98 (2008).