Computational Biology

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Showing 151 - 180 results of 184

2014

Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity.

Mol Oncol

V. Lang, C. Pallara, A. Zabala, S. Lobato-Gil, F. Lopitz-Otsoa, R. Farrás, R. Hjerpe, M. Torres-Ramos, L. Zabaleta, C. Blattner, R. T. Hay, R. Barrio, A. Carracedo, J. Fernandez-Recio, M. S. Rodríguez, and F. Aillet
Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc.

Proceedings of the National Academy of Sciences of the United States of America

A. Rosell, M. Meury, E. Alvarez-Marimon, M. Costa, L. Pérez-Cano, A. Zorzano, J. Fernández-Recio, M. Palacín, and D. Fotiadis
Blind prediction of interfacial water positions in CAPRI.

Proteins

M. F. Lensink, I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. M. J. J. Bonvin, M. Eisenstein, B. Jiménez-García, S. Grosdidier, A. Solernou, L. Pérez-Cano, C. Pallara, J. Fernández-Recio, J. Xu, P. Muthu, K. Praneeth Kilambi, J. J. Gray, S. Grudinin, G. Derevyanko, J. C. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D. M. Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. W. Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. J. Kundrotas, I. A. Vakser, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H. J. Wolfson, M. Zacharias, S. Qin, H-X. Zhou, S-Y. Huang, X. Zou, J. A. Wojdyla, C. Kleanthous, and S. J. Wodak

2013

Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

The Journal of Physical Chemistry B

G. R. Parra, R. Espada, I. E. Sánchez, M. J. Sippl, and D. U. Ferreiro
INSECT: IN-silico SEarch for Co-occurring Transcription factorsAbstract

Bioinformatics

C. O. Rohr, G. R. Parra, P. Yankilevich, and C. Perez-Castro
Structural prediction and characterization of protein-RNA interactions

L. Pérez Cano
The scoring of poses in protein-protein docking: current capabilities and future directions.

BMC bioinformatics

I. H. Moal, M. Torchala, P. A. Bates, and J. Fernández-Recio
Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.

PLoS computational biology

R. Agius, M. Torchala, I. H. Moal, J. Fernández-Recio, and P. A. Bates
Conformational transitions in human translin enable nucleic acid binding.

Nucleic acids research

L. Pérez-Cano, E. Eliahoo, K. Lasker, H. J. Wolfson, F. Glaser, H. Manor, P. Bernadó, and J. Fernández-Recio
Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges.

Proteins

C. Pallara, B. Jiménez-García, L. Pérez-Cano, M. Romero-Durana, A. Solernou, S. Grosdidier, C. Pons, I. H. Moal, and J. Fernández-Recio
Scoring functions for protein-protein interactions.

Current opinion in structural biology

I. H. Moal, R. Moretti, D. Baker, and J. Fernández-Recio
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Proteins

R. Moretti, S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. G. L. M. Rodrigues, M. Trellet, A. M. J. J. Bonvin, M. Cui, M. Rooman, D. Gillis, Y. Dehouck, I. Moal, M. Romero-Durana, L. Pérez-Cano, C. Pallara, B. Jimenez, J. Fernández-Recio, S. Flores, M. Pacella, K. Praneeth Kilambi, J. J. Gray, P. Popov, S. Grudinin, J. Esquivel-Rodríguez, D. Kihara, N. Zhao, D. Korkin, X. Zhu, O. N. A. Demerdash, J. C. Mitchell, E. Kanamori, Y. Tsuchiya, H. Nakamura, H. Lee, H. Park, C. Seok, J. Sarmiento, S. Liang, S. Teraguchi, D. M. Standley, H. Shimoyama, G. Terashi, M. Takeda-Shitaka, M. Iwadate, H. Umeyama, D. Beglov, D. R. Hall, D. Kozakov, S. Vajda, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, Y. Huang, H. Li, X. Yang, X. Ji, S. Liu, Y. Xiao, M. Zacharias, S. Qin, H-X. Zhou, S-Y. Huang, X. Zou, S. Velankar, J. Janin, S. J. Wodak, and D. Baker
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

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