Computational Biology

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Mostrando 151 - 172 resultados de 172

2013

Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD.

PLoS pathogens

Y. Chen, I. Tascón, R. M. Neunuebel, C. Pallara, J. Brady, L. N. Kinch, J. Fernández-Recio, A. L. Rojas, M. P. Machner, and A. Hierro
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
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations

Journal of Chemical Theory and Computation

A. Emperador, A. Solernou, P. Sfriso, C. Pons, J L. Gelpí, J. Fernández-Recio, and M. Orozco
SwarmDock: a server for flexible protein-protein docking.

Bioinformatics (Oxford, England)

M. Torchala, I. H. Moal, R. A. G. Chaleil, J. Fernández-Recio, and P. A. Bates

2012

Protein frustratometer: a tool to localize energetic frustration in protein molecules

Nucleic Acids Research

M.. Jenik, G. R. Parra, L.. G. Radusky, A.. Turjanski, P.. G. Wolynes, and D.. U. Ferreiro
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
Theory and simulation: complexity and emergence.

Current opinion in structural biology

J. Fernández-Recio, and C. Verma
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
Protein-protein docking and hot-spot prediction for drug discovery.

Current pharmaceutical design

S. Grosdidier, and J. Fernández-Recio
Allosteric conversation in the androgen receptor ligand-binding domain surfaces.

Molecular endocrinology (Baltimore, Md.)

S. Grosdidier, L. R. Carbó, V. Buzón, G. Brooke, P. Nguyen, J. D. Baxter, C. Bevan, P. Webb, E. Estébanez-Perpiñá, and J. Fernández-Recio
Cell-Dock: high-performance protein-protein docking.

Bioinformatics (Oxford, England)

C. Pons, D. Jiménez-González, C. González-Álvarez, H. Servat, D. Cabrera-Benítez, X. Aguilar, and J. Fernández-Recio
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models.

Bioinformatics (Oxford, England)

I. H. Moal, and J. Fernández-Recio

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
Prediction of protein binding sites and hot spots

WIREs Comput. Mol. Sci.

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
pyDockCG: new coarse-grained potential for protein-protein docking.

The journal of physical chemistry. B

A. Solernou, and J. Fernández-Recio
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

2010

Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data

C. Pons, M. D'Abramo, D.I. Svergun, M. Orozco, P. Bernadó, and J. Fernández-Recio

2009

On the use of low resolution data to improve structure predictions of proteins and protein complexes

M. D'Abramo, T. Meyer, P. Bernadó, J. Fernández-Recio, and M. Orozco

2007

Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization

J. Fort, L. R. de la Ballina, HE. Burghardt, C. Ferrer-Costa, J. Turnay, C. Ferrer-Orta, I. Usón, A. Zorzano, J. Fernández-Recio, PL. Fernández, M. Orozco, M. A. Lizarbe, I. Fita, and M. Palacín

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