Works by Fernandez-Fuentes, Narcis

Results: 58

Biochemical characterisation of a PL24 ulvan lyase from seaweed-associated Vibrio sp. FNV38.

Published in:

Journal of Applied Phycology, 2024, v. 36, n. 2, p. 697, doi. 10.1007/s10811-023-03136-3

By:

Rodrigues, Valerie J.;
Jouanneau, Diane;
Fernandez-Fuentes, Narcis;
Onime, Lucy A.;
Huws, Sharon A.;
Odaneth, Annamma A.;
Adams, Jessica M. M.

Publication type:

Article

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.

Published in:

Bioinformatics, 2018, v. 34, n. 4, p. 592, doi. 10.1093/bioinformatics/btx616

By:

Marín-López, Manuel Alejandro;
Planas-Iglesias, Joan;
Aguirre-Plans, Joaquim;
Bonet, Jaume;
Garcia-Garcia, Javier;
Fernandez-Fuentes, Narcis;
Oliva, Baldo

Publication type:

Article

MetaPred2CS: a sequence-based meta-predictor for protein--protein interactions of prokaryotic two-component system proteins.

Published in:

Bioinformatics, 2016, v. 32, n. 21, p. 3339, doi. 10.1093/bioinformatics/btw403

By:

Kara, Altan;
Vickers, Martin;
Swain, Martin;
Whitworth, David E.;
Fernandez-Fuentes, Narcis

Publication type:

Article

Knowledge-based modeling of peptides at protein interfaces: PiPreD.

Published in:

2015

By:

Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Product Review

Frag’r’Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1935, doi. 10.1093/bioinformatics/btu129

By:

Bonet, Jaume;
Segura, Joan;
Planas-Iglesias, Joan;
Oliva, Baldomero;
Fernandez-Fuentes, Narcis

Publication type:

Article

A holistic in silico approach to predict functional sites in protein structures.

Published in:

Bioinformatics, 2012, v. 28, n. 14, p. 1845, doi. 10.1093/bioinformatics/bts269

By:

Segura, Joan;
Jones, Pamela F.;
Fernandez-Fuentes, Narcis

Publication type:

Article

Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.

Published in:

Bioinformatics, 2007, v. 23, n. 19, p. 2558, doi. 10.1093/bioinformatics/btm377

By:

Narcis Fernandez-Fuentes;
Brajesh K. Rai;
Carlos J. Madrid-Aliste;
J. Eduardo Fajardo;
András Fiser

Publication type:

Article

A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses.

Published in:

Journal of Experimental Botany, 2021, v. 72, n. 2, p. 302, doi. 10.1093/jxb/eraa469

By:

Worthington, Margaret;
Perez, Juan Guillermo;
Mussurova, Saule;
Silva-Cordoba, Alexander;
Castiblanco, Valheria;
Arango, Juan Andres Cardoso;
Jones, Charlotte;
Fernandez-Fuentes, Narcis;
Skot, Leif;
Dyer, Sarah;
Tohme, Joe;
Palma, Federica Di;
Arango, Jacobo;
Armstead, Ian;
Vega, Jose J De

Publication type:

Article

Insight into the machinery that oils chromatin dynamics.

Published in:

Nucleus (1949-1034), 2016, v. 7, n. 6, p. 532, doi. 10.1080/19491034.2016.1255392

By:

Wright, Roni H. G.;
Fernandez-Fuentes, Narcis;
Oliva, Baldomero;
Beato, Miguel

Publication type:

Article

VORFFIP-Driven Dock: V-D<sup>2</sup>OCK, a Fast and Accurate Protein Docking Strategy.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0118107

By:

Segura, Joan;
Marín-López, Manuel Alejandro;
Jones, Pamela F.;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization.

Published in:

PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0043557

By:

Guney, Emre;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces.

Published in:

PLoS ONE, 2010, v. 5, n. 8, p. 1, doi. 10.1371/journal.pone.0012352

By:

Mora, Joan Segura;
Assi, Salam A.;
Fernandez-Fuentes, Narcis

Publication type:

Article

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus.

Published in:

NPJ Biofilms & Microbiomes, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41522-022-00320-0

By:

Oyama, Linda B.;
Olleik, Hamza;
Teixeira, Ana Carolina Nery;
Guidini, Matheus M.;
Pickup, James A.;
Hui, Brandon Yeo Pei;
Vidal, Nicolas;
Cookson, Alan R.;
Vallin, Hannah;
Wilkinson, Toby;
Bazzolli, Denise M. S.;
Richards, Jennifer;
Wootton, Mandy;
Mikut, Ralf;
Hilpert, Kai;
Maresca, Marc;
Perrier, Josette;
Hess, Matthias;
Mantovani, Hilario C.;
Fernandez-Fuentes, Narcis

Publication type:

Article

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0741-7

By:

Kara, Altan;
Vickers, Martin;
Swain, Martin;
Whitworth, David E.;
Fernandez-Fuentes, Narcis

Publication type:

Article

Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.

Published in:

Molecular Vision, 2022, v. 28, p. 57

By:

Panagiotou, Evangelia S.;
Fernandez-Fuentes, Narcis;
Farraj, Layal Abi;
McKibbin, Martin;
Elçioglu, Nursel H.;
Jafri, Hussain;
Cerman, Eren;
Parry, David A.;
Logan, Clare V.;
Johnson, Colin A.;
Inglehearn, Chris F.;
Toomes, Carmel;
Ali, Manir

Publication type:

Article

The rumen microbiome: an underexplored resource for novel antimicrobial discovery.

Published in:

NPJ Biofilms & Microbiomes, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41522-017-0042-1

By:

Oyama, Linda B.;
Girdwood, Susan E.;
Cookson, Alan R.;
Fernandez-Fuentes, Narcis;
Privé, Florence;
Vallin, Hannah E.;
Wilkinson, Toby J.;
Golyshin, Peter N.;
Golyshina, Olga V.;
Mikut, Ralf;
Hilpert, Kai;
Richards, Jennifer;
Wootton, Mandy;
Edwards, Joan E.;
Maresca, Marc;
Perrier, Josette;
Lundy, Fionnuala T.;
Luo, Yu;
Zhou, Mei;
Hess, Matthias

Publication type:

Article

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications.

Published in:

Bio-Algorithms & Med-Systems, 2014, v. 10, n. 4, p. 195, doi. 10.1515/bams-2014-0016

By:

Bonet, Jaume;
Fiser, Andras;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05707-2

By:

Quevedo, Camilo E.;
Cruz-Migoni, Abimael;
Bery, Nicolas;
Miller, Ami;
Tanaka, Tomoyuki;
Petch, Donna;
Bataille, Carole J. R.;
Lee, Lydia Y. W.;
Fallon, Phillip S.;
Tulmin, Hanna;
Ehebauer, Matthias T.;
Fernandez-Fuentes, Narcis;
Russell, Angela J.;
Carr, Stephen B.;
Phillips, Simon E. V.;
Rabbitts, Terence H.

Publication type:

Article

The GH51 α-L-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans.

Published in:

Biotechnology for Biofuels, 2016, v. 9, p. 1, doi. 10.1186/s13068-016-0550-x

By:

Bouraoui, Hanen;
Desrousseaux, Marie-Laure;
Ioannou, Eleni;
Alvira, Pablo;
Manaï, Mohamed;
Rémond, Caroline;
Dumon, Claire;
Fernandez-Fuentes, Narcis;
O'Donohue, Michael J.

Publication type:

Article

Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops.

Published in:

Proteins, 2005, v. 60, n. 4, p. 746, doi. 10.1002/prot.20516

By:

Fernandez-Fuentes, Narcis;
Querol, Enrique;
Aviles, Francesc X.;
Sternberg, Michael J. E.;
Oliva, Baldomero

Publication type:

Article

Classification of common functional loops of kinase super-families.

Published in:

Proteins, 2004, v. 56, n. 3, p. 539, doi. 10.1002/prot.20136

By:

Fernandez-Fuentes, Narcis;
Hermoso, Antoni;
Espadaler, Jordi;
Querol, Enrique;
Aviles, Francesc X.;
Oliva, Baldomero

Publication type:

Article

Methyl-CpG-binding (SmMBD2/3) and chromobox (SmCBX) proteins are required for neoblast proliferation and oviposition in the parasitic blood fluke Schistosoma mansoni.

Published in:

PLoS Pathogens, 2018, v. 14, n. 6, p. 1, doi. 10.1371/journal.ppat.1007107

By:

Geyer, Kathrin K.;
Munshi, Sabrina E.;
Whiteland, Helen L.;
Fernandez-Fuentes, Narcis;
Phillips, Dylan W.;
Hoffmann, Karl F.

Publication type:

Article

Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defects.

Published in:

Human Molecular Genetics, 2012, v. 21, n. 4, p. 776, doi. 10.1093/hmg/ddr509

By:

Khan, Kamron;
Logan, Clare V.;
McKibbin, Martin;
Sheridan, Eamonn;
Elçioglu, Nursel H.;
Yenice, Ozlem;
Parry, David A.;
Fernandez-Fuentes, Narcis;
Abdelhamed, Zakia I.A.;
Al-Maskari, Ahmed;
Poulter, James A.;
Mohamed, Moin D.;
Carr, Ian M.;
Morgan, Joanne E.;
Jafri, Hussain;
Raashid, Yasmin;
Taylor, Graham R.;
Johnson, Colin A.;
Inglehearn, Chris F.;
Toomes, Carmel

Publication type:

Article

Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita.

Published in:

Human Molecular Genetics, 2009, v. 18, n. 23, p. 4546, doi. 10.1093/hmg/ddp416

By:

Grozdanov, Petar N.;
Fernandez-Fuentes, Narcis;
Fiser, Andras;
Meier, U. Thomas

Publication type:

Article

Stabilisation of half MCM ring by Cdt1 during DNA insertion.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21932-8

By:

Guerrero-Puigdevall, Marina;
Fernandez-Fuentes, Narcis;
Frigola, Jordi

Publication type:

Article

Mining drug–target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab068

By:

Galletti, Cristiano;
Bota, Patricia Mirela;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

Published in:

Biochemical Society Transactions, 2016, v. 44, n. 3, p. 917, doi. 10.1042/BST20150001

By:

Poglayen, Daniel;
Marín-Lৰpez, Manuel Alejandro;
Bonet, Jaume;
Fornes, Oriol;
Garcia-Garcia, Javier;
Planas-Iglesias, Joan;
Segura, Joan;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential.

Published in:

BMC Microbiology, 2021, v. 21, n. 1, p. 1, doi. 10.1186/s12866-021-02172-8

By:

Onime, Lucy A.;
Oyama, Linda B.;
Thomas, Benjamin J.;
Gani, Jurnorain;
Alexander, Peter;
Waddams, Kate E.;
Cookson, Alan;
Fernandez-Fuentes, Narcis;
Creevey, Christopher J.;
Huws, Sharon A.

Publication type:

Article

Structural Characteristics of Novel Protein Folds.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000750

By:

Fernandez-Fuentes, Narcis;
Dybas, Joseph M.;
Fiser, Andras

Publication type:

Article

Computational Design and Evaluation of Peptides to Target SARS-CoV-2 Spike–ACE2 Interaction.

Published in:

Molecules, 2025, v. 30, n. 8, p. 1750, doi. 10.3390/molecules30081750

By:

Almabhouh, Saja;
Cecon, Erika;
Basubas, Florence;
Molina-Fernandez, Ruben;
Maciej Stepniewski, Tomasz;
Selent, Jana;
Jockers, Ralf;
Rahmeh, Amal;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design.

Published in:

Pathogens, 2021, v. 10, n. 12, p. 1599, doi. 10.3390/pathogens10121599

By:

Düzgüneş, Nejat;
Fernandez-Fuentes, Narcis;
Konopka, Krystyna

Publication type:

Article

Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth.

Published in:

Plants, People, Planet, 2020, v. 2, n. 3, p. 229, doi. 10.1002/ppp3.10086

By:

De Vega, Jose J.;
Davey, Robert P.;
Duitama, Jorge;
Escobar, Dairo;
Cristancho‐Ardila, Marco A.;
Etherington, Graham J.;
Minotto, Alice;
Arenas‐Suarez, Nelson E.;
Pineda‐Cardenas, Juan D.;
Correa‐Alvarez, Javier;
Camargo Rodriguez, Anyela V.;
Haerty, Wilfried;
Mallarino‐Robayo, Juan P.;
Barreto‐Hernandez, Emiliano;
Muñoz‐Torres, Monica;
Fernandez‐Fuentes, Narcis;
Di Palma, Federica

Publication type:

Article

Halotolerant bacterial endophyte Bacillus velezensi s CBE mediates abiotic stress tolerance with minimal transcriptional modifications in Brachypodium distachyon.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2024.1485391

By:

Abd El-Daim, Islam A.;
Raynes, Gareth;
Fernandez-Fuentes, Narcis;
Hawkins, Sarah;
Cookson, Alan;
Farrar, Kerrie

Publication type:

Article

Structure-based learning to predict and model protein--DNA interactions and transcription-factor co-operativity in cis-regulatory elements.

Published in:

NAR Genomics & Bioinformatics, 2024, v. 6, n. 2, p. 1, doi. 10.1093/nargab/lqae068

By:

Fornes, Oriol;
Meseguer, Alberto;
Aguirre-Plans, Joachim;
Gohl, Patrick;
Bota, Patricia M.;
Molina-Fernández, Ruben;
Bonet, Jaume;
Chinchilla-Hernandez, Altair;
Pegenaute, Ferran;
Gallego, Oriol;
Fernandez-Fuentes, Narcis;
Oliva, Baldo

Publication type:

Article

ArchDB: automated protein loop classification as a tool for structural genomics.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d185

By:

Espadaler, Jordi;
Fernandez‐Fuentes, Narcis;
Hermoso, Antonio;
Querol, Enrique;
Aviles, Francesc X.;
Sternberg, Michael J. E.;
Oliva, Baldomero

Publication type:

Article

In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan.

Published in:

PLoS ONE, 2020, v. 15, n. 2, p. 1, doi. 10.1371/journal.pone.0228926

By:

Jorba, Guillem;
Aguirre-Plans, Joaquim;
Junet, Valentin;
Segú-Vergés, Cristina;
Ruiz, José Luis;
Pujol, Albert;
Fernández-Fuentes, Narcís;
Mas, José Manuel;
Oliva, Baldo

Publication type:

Article

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne).

Published in:

PLoS ONE, 2019, v. 14, n. 7, p. 1, doi. 10.1371/journal.pone.0220518

By:

Fradera-Sola, Albert;
Thomas, Ann;
Gasior, Dagmara;
Harper, John;
Hegarty, Matthew;
Armstead, Ian;
Fernandez-Fuentes, Narcis

Publication type:

Article

An ensemble learning approach for modeling the systems biology of drug-induced injury.

Published in:

Biology Direct, 2021, v. 16, n. 1, p. 1, doi. 10.1186/s13062-020-00288-x

By:

Aguirre-Plans, Joaquim;
Piñero, Janet;
Souza, Terezinha;
Callegaro, Giulia;
Kunnen, Steven J.;
Sanz, Ferran;
Fernandez-Fuentes, Narcis;
Furlong, Laura I.;
Guney, Emre;
Oliva, Baldo

Publication type:

Article

A Collection of Designed Peptides to Target SARS-CoV-2 Spike RBD—ACE2 Interaction.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 21, p. 11627, doi. 10.3390/ijms222111627

By:

Fernandez-Fuentes, Narcis;
Molina, Ruben;
Oliva, Baldo

Publication type:

Article

Evaluation of Computationally Designed Peptides against TWEAK, a Cytokine of the Tumour Necrosis Factor Ligand Family.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 3, p. 1066, doi. 10.3390/ijms22031066

By:

Badia-Villanueva, Miriam;
Defaus, Sira;
Foj, Ruben;
Andreu, David;
Oliva, Baldo;
Sierra, Angels;
Fernandez-Fuentes, Narcis

Publication type:

Article

Saturating representation of loop conformational fragments in structure databanks.

Published in:

BMC Structural Biology, 2006, v. 6, p. 15, doi. 10.1186/1472-6807-6-15

By:

Fernandez-Fuentes, Narcis;
Fiser, András

Publication type:

Article

SBILib: a handle for protein modeling and engineering.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad613

By:

Gohl, Patrick;
Bonet, Jaume;
Fornes, Oriol;
Planas-Iglesias, Joan;
Fernandez-Fuentes, Narcís;
Oliva, Baldo

Publication type:

Article

Human IgG<sub>1</sub> Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment.

Published in:

PLoS Neglected Tropical Diseases, 2015, v. 9, n. 7, p. 1, doi. 10.1371/journal.pntd.0003920

By:

Chalmers, Iain W.;
Fitzsimmons, Colin M.;
Brown, Martha;
Pierrot, Christine;
Jones, Frances M.;
Wawrzyniak, Jakub M.;
Fernandez-Fuentes, Narcis;
Tukahebwa, Edridah M.;
Dunne, David W.;
Khalife, Jamal;
Hoffmann, Karl F.

Publication type:

Article

Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 10, p. 2112, doi. 10.1002/pro.3930

By:

Meseguer, Alberto;
Dominguez, Lluis;
Bota, Patricia M.;
Aguirre‐Plans, Joaquim;
Bonet, Jaume;
Fernandez‐Fuentes, Narcis;
Oliva, Baldo

Publication type:

Article

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes.

Published in:

Frontiers in Plant Science, 2021, v. 11, p. N.PAG, doi. 10.3389/fpls.2021.637956

By:

Jones, Charlotte;
De Vega, Jose;
Worthington, Margaret;
Thomas, Ann;
Gasior, Dagmara;
Harper, John;
Doonan, John;
Fu, Yuan;
Bosch, Maurice;
Corke, Fiona;
Arango, Jacobo;
Cardoso, Juan Andres;
de la Cruz Jimenez, Juan;
Armstead, Ian;
Fernandez-Fuentes, Narcis

Publication type:

Article

A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.

Published in:

Frontiers in Plant Science, 2020, v. 11, p. N.PAG, doi. 10.3389/fpls.2020.586870

By:

Nibau, Candida;
Dadarou, Despoina;
Kargios, Nestoras;
Mallioura, Areti;
Fernandez-Fuentes, Narcis;
Cavallari, Nicola;
Doonan, John H.

Publication type:

Article

ArchDB 2014: structural classification of loops in proteins.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D315, doi. 10.1093/nar/gkt1189

By:

Bonet, Jaume;
Planas-Iglesias, Joan;
Garcia-Garcia, Javier;
Marín-López, Manuel A.;
Fernandez-Fuentes, Narcis;
Oliva, Baldo

Publication type:

Article

CAPS-DB: a structural classification of helix-capping motifs.

Published in:

Nucleic Acids Research, 2012, p. D479, doi. 10.1093/nar/gkr879

By:

Segura, Joan;
Oliva, Baldomero;
Fernandez-Fuentes, Narcis

Publication type:

Article

PCRPi-DB: a database of computationally annotated hot spots in protein interfaces.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D755, doi. 10.1093/nar/gkq1068

By:

Segura, Joan;
Fernandez-Fuentes, Narcis

Publication type:

Article

Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 18, p. 6124, doi. 10.1093/nar/gkq356

By:

Bowers, Sarion R.;
Calero-Nieto, Fernando J.;
Valeaux, Stephanie;
Fernandez-Fuentes, Narcis;
Cockerill, Peter N.

Publication type:

Article