Computational Biology

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Showing 121 - 150 results of 180

2015

Repeat proteins challenge the concept of structural domains

Biochemical Society Transactions

R. Espada, G. R. Parra, M. J. Sippl, T. Mora, A. M. Walczak, and D. U. Ferreiro
Capturing coevolutionary signals inrepeat proteins

BMC Bioinformatics

R. Espada, G. R. Parra, T. Mora, A. M. Walczak, and D. U. Ferreiro
Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

PLOS Computational Biology

G. R. Parra, R. Espada, N. Verstraete, and D. U. Ferreiro
Conformational heterogeneity enhances protein-protein recognition

XXXVIII Congreso SEBBM. Valencia

C.. Pallara, and J. Fernández-Recio
Identification of near-native protein-protein docking models using structural clustering

XXXVIII Congreso SEBBM. Valencia

S.. Mares-Sámano, and J. Fernández-Recio
Hot-spot interface predictions to identify edgetic mutations

XXXVIII Congreso SEBBM. Valencia

D. Barradas-Bautista, and J. Fernández-Recio
LightDock: a novel protein-protein docking framework for the new challenges in the interactomics era

XXXVIII Congreso SEBBM. Valencia

B.. Jiménez-García, and J. Fernández-Recio
Computational structural analysis and energetics of protein interactions: identifying disease-associated residues

XXXVIII Congreso SEBBM. Valencia

J. Fernández-Recio
Expanding template-based protein-protein complex prediction using ab-initio docking

29th Annual symposium of the Protein Society. Barcelona

S.. Mares-Sámano, L.A.. Rodríguez-Lumbreras, and J. Fernández-Recio
Protein plasticity improves protein-protein binding description

29th Annual symposium of the Protein Society. Barcelona

C.. Pallara, and J. Fernández-Recio
Identification of the structural and energetic basis of MEK1 pathological mutations: a Molecular Dynamics and Metadynamics study

XXII Jornades de Biologia Molecular SCB. Barcelona

C.. Pallara, and J. Fernández-Recio
Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor.

BBA - Biochimica et Biophysica Acta

P. Bernal-Bayard, C. Pallara, C. M Castell, F. P. Molina-Heredia, J. Fernandez-Recio, M. Hervás, and J. A. Navarro
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
pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

Nucleic Acids Research

B. Jiménez-García, C. Pons, D. I. Svergun, P. Bernadó, and J. Fernandez-Recio
EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF.

Oncotarget

F. Khayati, L. Pérez-Cano, K. Maouche, A. Sadoux, Z. Boutalbi, M-P. Podgorniak, U. Maskos, N. Setterblad, A. Janin, F. Calvo, C. Lebbé, S. Menashi, J. Fernandez-Recio, and S. Mourah
Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction.

Thrombosis and Haemostasis

S. Somajo, J. Ahnström, J. Fernandez-Recio, M. Gierula, B. O. Villoutreix, and B. Dahlbäck
Inferring the microscopic surface energy of protein-protein interfaces from mutation data.

Proteins

I. H. Moal, J. Dapkūnas, and J. Fernandez-Recio
Comment on 'protein-protein binding affinity prediction from amino acid sequence'.

Bioinformatics

I. H. Moal, and J. Fernandez-Recio
CCharPPI web server: computational characterization of protein-protein interactions from structure.

Bioinformatics

I. H. Moal, B. Jiménez-García, and J. Fernandez-Recio

2014

RepeatsDB: a database of tandem repeat protein structures

Nucleic Acids Research

T. Di Domenico, E. Potenza, I. Walsh, G. R. Parra, M. Giollo, G. Minervini, D. Piovesan, A. Ihsan, C. Ferrari, A. V. Kajava, and S. C. E. Tosatto
EVALUATING SCORING FUNCTIONS FOR PROTEIN-PROTEIN DOCKING

3DSIG: STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS, Boston (US)

I.H. Moal, and J. Fernández-Recio
Conformational selection mechanism in protein-protein association: insights from docking

II Jornada de Bioinformàtica i Biologia Computacional (Barcelona)

C.. Pallara, M.. Rueda, and J. Fernández-Recio
Functional characterization and modeling of protein-protein interfaces: lessons from docking

Protein-Protein Interactions on the Genomic Scale. Paris (France)

J. Fernández-Recio
Structure and energetics of protein-RNA interactions: new insights from docking predictions.

XIV Congress of the Spanish Biophysical Society. Alcalá de Henares (Spain).

L.. Pérez-Cano, M. Romero-Durana, and J. Fernández-Recio
EMMPRIN/CD147 is a co-receptor for VEGFR-2 in tumor angiogenesis: towards its inhibition.

Fund. Clin. Pharm.

F.. Khayati, J. Fernández-Recio, L.. Pérez, B.. Villoutreix, F.. Calvo, C.. Lebbe, S.. Menashi, and S.. Mourah
Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.

Proc Natl Acad Sci U S A

M. Lucas, A. H. Gaspar, C. Pallara, A. Lucely Rojas, J. Fernandez-Recio, M. P. Machner, and A. Hierro
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

Pages