Publications

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P
Solernou, A. & Fernández-Recio, J. pyDockCG: new coarse-grained potential for protein-protein docking. The journal of physical chemistry. B 115, 6032-9 (2011).
Pérez-Cano, L., Jiménez-García, B. & Fernández-Recio, J. A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data. Proteins 80, 1872-82 (2012).
Pons, C., Glaser, F. & Fernandez-Recio, J. Prediction of protein-binding areas by small-world residue networks and application to docking. BMC bioinformatics 12, 378 (2011).
N
Flores, O. & Orozco, M. nucleR: a package for non-parametric nucleosome positioning. Bioinformatics (Oxford, England) 27, 2149-50 (2011).
M
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).
I
Cho, A.E., Guallar, V., Berne, B.J. & Friesner, R.A. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of computational chemistry 26, 915-31 (2005).
E
Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J.M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R.R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M.L., Gelpí, J.L., Orozco, M., Valencia, A., van Berkum, N.L., Lajoie, B.R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S.E., Guigó, R. & Gingeras, T.R. Evidence for transcript networks composed of chimeric RNAs in human cells. PloS one 7, e28213 (2012).
C
Guallar, V., Jacobson, M., McDermott, A. & Friesner, R.A. Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
B
Guallar, V. & Borrelli, K. A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding. Proceedings of the National Academy of Sciences of the United States of America 102, 3954-9 (2005).