Publications

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2015

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Journal of Molecular Biology

T. Vreven, I. H. Moal, A. Vangone, B. G. Pierce, P. L. Kastritis, M. Torchala, R. Chaleil, B. Jiménez-García, P. A. Bates, J. Fernandez-Recio, A. M. J. J. Bonvin, and Z. Weng
Exploiting Asynchrony from Exact Forward Recovery for DUE in Iterative Solvers

SC'15 - Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

L. Jaulmes, M. Casas, M. Moreto, E. Ayguade, J. Labarta, and M. Valero

2013

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

Bioinformatics (Oxford, England)

B. Jiménez-García, C. Pons, and J. Fernández-Recio
Exploration of conformational transition pathways from coarse-grained simulations.

Bioinformatics (Oxford, England)

P. Sfriso, A. Hospital, A. Emperador, and M. Orozco

2012

A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data.

Proteins

L. Pérez-Cano, B. Jiménez-García, and J. Fernández-Recio
Evidence for transcript networks composed of chimeric RNAs in human cells.

PloS one

S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix, C. Borel, J. M. Mudge, C. Howald, S. Foissac, C. Ucla, J. Chrast, P. Ribeca, D. Martin, R. R. Murray, X. Yang, L. Ghamsari, C. Lin, I. Bell, E. Dumais, J. Drenkow, M. L. Tress, J L. Gelpí, M. Orozco, A. Valencia, N. L. van Berkum, B. R. Lajoie, M. Vidal, J. Stamatoyannopoulos, P. Batut, A. Dobin, J. Harrow, T. Hubbard, J. Dekker, A. Frankish, K. Salehi-Ashtiani, A. Reymond, S. E. Antonarakis, R. Guigó, and T. R. Gingeras

2011

Prediction of protein-binding areas by small-world residue networks and application to docking.

BMC bioinformatics

C. Pons, F. Glaser, and J. Fernández-Recio
Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM).

Molecular diversity

M. Fernández, J. Caballero, L. Fernández, and A. Sarai
pyDockCG: new coarse-grained potential for protein-protein docking.

The journal of physical chemistry. B

A. Solernou, and J. Fernández-Recio
Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine.

The Journal of biological chemistry

A. Hernández-Ortega, F. Lucas, P. Ferreira, M. Medina, V. Guallar, and A. T. Martínez

Pages