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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

2013

The dynamic view of proteins: comment on "Comparing proteins to their internal dynamics: exploring structure-function relationships beyond static structural alignments".

Physics of life reviews

M. Orozco

2012

H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?

Proteins

D. Masone, I. Cabeza de Vaca, C. Pons, J. Fernández-Recio, and V. Guallar
Established and emerging trends in computational drug discovery in the structural genomics era.

Chemistry & biology

O. Taboureau, J. B. Baell, J. Fernández-Recio, and B. O. Villoutreix
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

Bioinformatics (Oxford, England)

A. Hospital, P. Andrio, C. Fenollosa, D. Cicin-Sain, M. Orozco, and J L. Gelpí

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
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Journal of molecular biology

S. J. Fleishman, T. A. Whitehead, E-M. Strauch, J. E. Corn, S. Qin, H-X. Zhou, J. C. Mitchell, O. N. A. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J-su. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Azé, S. Soner, S K. Ovali, P. Ozbek, N B. Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Pérez-Cano, C. Pons, J. Fernández-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li, D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Potapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M. Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodríguez, D. Kihara, B. P. Stranges, R. Jacak, B. Kuhlman, S-Y. Huang, X. Zou, S. J. Wodak, J. Janin, and D. Baker
LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.

PloS one

L. Helft, V. Reddy, X. Chen, T. Koller, L. Federici, J. Fernández-Recio, R. Gupta, and A. Bent
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking.

Journal of chemical information and modeling

C. Pons, D. Talavera, X. de la Cruz, M. Orozco, and J. Fernández-Recio
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks.

Structure (London, England : 1993)

A. Stein, M. Rueda, A. Panjkovich, M. Orozco, and P. Aloy

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