Browsing by Author "Fernández-Recio, Juan"
Now showing items 1-20 of 28
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A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining
(Wiley, 2017-07)
Article
Open AccessProtein-protein interactions play fundamental roles in biological processes including signaling, metabolism, and trafficking. While the structure of a protein complex reveals crucial details about the interaction, it is ... -
Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction
(Schattauer, 2015-05)
Article
Open AccessProtein S functions as a cofactor for tissue factor pathway inhibitor (TFPI) and activated protein C (APC). The sex hormone binding globulin (SHBG)-like region of protein S, consisting of two laminin G-like domains (LG1 ... -
Blind prediction of interfacial water positions in CAPRI
(Wiley, 2014-04)
Article
Open AccessWe report the first assessment of blind predictions of water positions at protein–protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting ... -
CCharPPI web server: computational characterization of protein–protein interactions from structure
(Oxford University Press, 2014-09-02)
Article
Open AccessThe atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization ... -
CCharPPI web server: computational characterization of protein–protein interactions from structure
(Oxford Journals, 2015-01-01)
Article
Open AccessThe atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization ... -
Characteritzation of pathological mutations affecting protein-protein interactions for drug discovery
(Barcelona Supercomputing Center, 2018-04-24)
Conference report
Open Access -
Comment on ‘protein–protein binding affinity prediction from amino acid sequence
(2014-10-17)
Article
Open AccessPredicting the strength of interactions between globular proteins is a central and important topic in structural bioinformatics (Moal et al., 2013). The amino acid sequence represents the chemical bonding in a protein ... -
Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein–Protein Encounters
(American Chemical Society, 2016-06-20)
Article
Open AccessTo understand cellular processes at the molecular level we need to improve our knowledge of protein−protein interactions, from a structural, mechanistic, and energetic point of view. Current theoretical studies and ... -
Docking through democracy re-ranking protein-protein decoys with a voting system
(Barcelona Supercomputing Center, 2015-05-05)
Conference report
Open AccessWe have develop a machine learning framework to enhance protein-protein docking results, using Schulze voting method applied to several models from Support Vector machines. -
Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations
(Public Library of Science, 2017-08-25)
Article
Open AccessNext-generation sequencing (NGS) technologies are providing genomic information for an increasing number of healthy individuals and patient populations. In the context of the large amount of generated genomic data that is ... -
EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF
(Wiley, 2015-03-23)
Article
Open AccessEMMPRIN/CD147 is mainly known for its protease inducing function but a role in promoting tumor angiogenesis has also been demonstrated. This study provides evidence that EMMPRIN is a new coreceptor for the VEGFR-2 tyrosine ... -
Hot-spot analysis for drug discovery targeting protein-protein interactions
(Taylor & Francis, 2018-01-29)
Article
Open AccessIntroduction: Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions ... -
Inferring the microscopic surface energy of protein-protein interfaces from mutation data
(Wiley, 2015-04)
Article
Open AccessMutations at protein-protein recognition sites alter binding strength by altering the chemical nature of the interacting surfaces. We present a simple surface energy model, parameterised with empirical DDG values, yielding ... -
Interaction of photosystem I from Phaeodactylum tricornutum with plastocyanins as compared with its native cytochrome c6: Reunion with a lost donor
(Elsevier, 2015-12)
Article
Open AccessIn the Phaeodactylum tricornutum alga, as in most diatoms, cytochrome c6 is the only electron donor to photosystem I, and thus they lack plastocyanin as an alternative electron carrier. We have investigated, by using ... -
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection
(Oxford University Press, 2017-02-14)
Article
Open AccessMotivation: In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can ... -
LightDock: a new multi-scale approach to protein–protein docking
(Oxford University Press, 2017-09-04)
Article
Open AccessComputational prediction of protein–protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult ... -
Modeling of protein complexes and molecular assemblies with pyDock
(Springer Link, 2020)
Part of book or chapter of book
Open AccessThe study of the 3D structural details of protein interactions is essential to understand biomolecular functions at the molecular level. In this context, the limited availability of experimental structures of protein–protein ... -
Optimization of protein–protein docking for predicting Fc–protein interactions
(Wiley, 2016-07-22)
Article
Open AccessThe antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization ... -
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
(Wiley, 2016-06-01)
Article
Open AccessWe present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets ... -
pyDock scoring for the new modeling challenges in docking: protein-peptide, homo-multimers and domain-domain interactions
(Wiley, 2016-10-04)
Article
Open AccessThe 6th CAPRI edition included new modelling challenges, such as the prediction of protein-peptide complexes, and the modelling of homo-oligomers and domain-domain interactions as part of the first joint CASP-CAPRI experiment. ...
