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1

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

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,

Journal:

npj Biofilms and Microbiomes

Année:

2017

Langue:

english

Fichier:

PDF, 3.24 MB

english, 2017

2

Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription

Sharma, Priyanka, Lioutas, Antonios, Fernandez-Fuentes, Narcis, Quilez, Javier, Carbonell-Caballero, José, Wright, Roni H.G., Di Vona, Chiara, Le Dily, François, Schüller, Roland, Eick, Dirk, Oliva, B

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 5.28 MB

english, 2018

3

In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm

Artigas, Laura, Coma, Mireia, Matos-Filipe, Pedro, Aguirre-Plans, Joaquim, FarrÃ©s, Judith, Valls, Raquel, Fernandez-Fuentes, Narcis, de la Haba-Rodriguez, Juan, Olvera, Alex, Barbera, Jose, Morales,

Journal:

Année:

2020

Fichier:

PDF, 2.08 MB

2020

4

Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams

Joan Segura, Pamela F Jones, Narcis Fernandez-Fuentes

Journal:

BMC Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 434 KB

english, 2011

5

Saturating representation of loop conformational fragments in structure databanks

Narcis Fernandez-Fuentes, András Fiser

Journal:

BMC Structural Biology

Année:

2006

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2006

6

Classification of common functional loops of kinase super-families

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 432 KB

english, 2004

7

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

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 631 KB

english, 2005

8

Homozygous Mutations in PXDN Cause Congenital Cataract, Corneal Opacity, and Developmental Glaucoma

Kamron Khan, Adam Rudkin, David A. Parry, Kathryn P. Burdon, Martin McKibbin, Clare V. Logan, Zakia I.A. Abdelhamed, James S. Muecke, Narcis Fernandez-Fuentes, Kate J. Laurie, Mike Shires, Rhys Fogart

Journal:

The American Journal of Human Genetics

Année:

2011

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2011

9

Automated detection of remote homology

Sabine Dietmann, Narcis Fernandez-Fuentes, Liisa Holm

Journal:

Current Opinion in Structural Biology

Année:

2002

Langue:

english

Fichier:

PDF, 61 KB

english, 2002

10

Structural Characteristics of Novel Protein Folds

Fernandez-Fuentes, Narcis, Dybas, Joseph M., Fiser, Andras, Nussinov, Ruth

Journal:

PLoS Computational Biology

Année:

2010

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2010

11

Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database

Bourgeas, Raphaël, Basse, Marie-Jeanne, Morelli, Xavier, Roche, Philippe, Fernandez-Fuentes, Narcis

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 752 KB

english, 2010

12

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

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

Journal:

Bio-Algorithms and Med-Systems

Année:

2014

Langue:

english

Fichier:

PDF, 5.42 MB

english, 2014

13

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

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

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 572 KB

english, 2015

14

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, S

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2016

15

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

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

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 216 KB

english, 2016

16

Insight into the machinery that oils chromatin dynamics

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

Journal:

Nucleus (Landes Bioscience)

Année:

2016

Langue:

english

Fichier:

PDF, 2.44 MB

english, 2016

17

iFrag: A Protein–Protein Interface Prediction Server Based on Sequence Fragments

Garcia-Garcia, Javier, Valls-Comamala, Victòria, Guney, Emre, Andreu, David, Muñoz, Francisco J., Fernandez-Fuentes, Narcis, Oliva, Baldo

Journal:

Journal of Molecular Biology

Année:

2017

Langue:

english

Fichier:

PDF, 516 KB

english, 2017

18

Genetic and functional characterization of disease associations explains comorbidity

Rubio-Perez, Carlota, Guney, Emre, Aguilar, Daniel, Piñero, Janet, Garcia-Garcia, Javier, Iadarola, Barbara, Sanz, Ferran, Fernandez-Fuentes, Narcís, Furlong, Laura I., Oliva, Baldo

Journal:

Scientific Reports

Année:

2017

Langue:

english

Fichier:

PDF, 3.43 MB

english, 2017

19

Draft Genome Assemblies of Xylose-Utilizing Candida tropicalis and Candida boidinii with Potential Application in Biochemical and Biofuel Production

Somani, Abhishek, Smith, Daniel, Hegarty, Matthew, Fernandez-Fuentes, Narcis, Ravella, Sreenivas R., Gallagher, Joe A., Bryant, David N.

Journal:

Genome Announcements

Année:

2018

Langue:

english

Fichier:

PDF, 126 KB

english, 2018

20

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

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

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 378 KB

english, 2018

21

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

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

Journal:

Biotechnology for Biofuels

Année:

2016

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2016

22

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

Korpar, Matija, Šošić, Martin, Blažeka, Dino, Šikić, Mile, Fernandez-Fuentes, Narcis

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

23

Structural and Functional Roles of Coevolved Sites in Proteins

Chakrabarti, Saikat, Panchenko, Anna R., Fernandez-Fuentes, Narcis

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1006 KB

english, 2010

24

Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling

MacDonald, James T., Kelley, Lawrence A., Freemont, Paul S., Fernandez-Fuentes, Narcis

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.40 MB

english, 2013

25

Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids

Chee, Sharon Min Qi, Wongsantichon, Jantana, Siau, Jiawei, Thean, Dawn, Ferrer, Fernando, Robinson, Robert C., Lane, David P., Brown, Christopher J., Ghadessy, Farid J., Fernandez-Fuentes, Narcis

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 5.25 MB

english, 2017

26

Exchanging Murine and Human Immunoglobulin Constant Chains Affects the Kinetics and Thermodynamics of Antigen Binding and Chimeric Antibody Autoreactivity

Torres, Marcela, Fernandez-Fuentes, Narcis, Fiser, András, Casadevall, Arturo, Khan, Wasif

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2007

27

A Biochemical Genomics Screen for Substrates of Ste20p Kinase Enables the In Silico Prediction of Novel Substrates

Annan, Robert B., Lee, Anna Y., Reid, Ian D., Sayad, Azin, Whiteway, Malcolm, Hallett, Michael, Thomas, David Y., Fernandez-Fuentes, Narcis

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2009

28

MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography

Konagurthu, Arun S., Reboul, Cyril F., Schmidberger, Jason W., Irving, James A., Lesk, Arthur M., Stuckey, Peter J., Whisstock, James C., Buckle, Ashley M., Fernandez-Fuentes, Narcis

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2010

29

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

de Vries, Sjoerd J., Bonvin, Alexandre M. J. J., Fernandez-Fuentes, Narcis

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 246 KB

english, 2011

30

mRNA Display Selection of an Optimized MDM2-Binding Peptide That Potently Inhibits MDM2-p53 Interaction

Shiheido, Hirokazu, Takashima, Hideaki, Doi, Nobuhide, Yanagawa, Hiroshi, Fernandez-Fuentes, Narcis

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 728 KB

english, 2011

31

Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins

Riihimäki, Tiina A., Kukkurainen, Sampo, Varjonen, Suvi, Hörhä, Jarno, Nyholm, Thomas K. M., Kulomaa, Markku S., Hytönen, Vesa P., Fernandez-Fuentes, Narcis

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 793 KB

english, 2011

32

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

Hensen, Ulf, Meyer, Tim, Haas, Jürgen, Rex, René, Vriend, Gert, Grubmüller, Helmut, Fernandez-Fuentes, Narcis

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 859 KB

english, 2012

33

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Suzuki, Shuji, Ishida, Takashi, Kurokawa, Ken, Akiyama, Yutaka, Fernandez-Fuentes, Narcis

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 1.54 MB

english, 2012

34

Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features

Aguilar, Daniel, Oliva, Baldo, Marino Buslje, Cristina, Fernandez-Fuentes, Narcis

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 819 KB

english, 2012

35

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

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

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 588 KB

english, 2012

36

HIPdb: A Database of Experimentally Validated HIV Inhibiting Peptides

Qureshi, Abid, Thakur, Nishant, Kumar, Manoj, Fernandez-Fuentes, Narcis

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 287 KB

english, 2013

37

Towards Improved Quality of GPCR Models by Usage of Multiple Templates and Profile-Profile Comparison

Latek, Dorota, Pasznik, Pawel, Carlomagno, Teresa, Filipek, Slawomir, Fernandez-Fuentes, Narcis

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 679 KB

english, 2013

38

Human Serum Albumin and p53-Activating Peptide Fusion Protein Is Able to Promote Apoptosis and Deliver Fatty Acid-Modified Molecules

Joshi, Michelle R., Yao, Nianhuan, Myers, Kenneth A., Li, Zhiyu, Fernandez-Fuentes, Narcis

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2013

39

VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking Strategy

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

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2015

40

RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat –Omics Data

Vincent, Jonathan, Martre, Pierre, Gouriou, Benjamin, Ravel, Catherine, Dai, Zhanwu, Petit, Jean-Marc, Pailloux, Marie, Fernandez-Fuentes, Narcis

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 3.54 MB

english, 2015

41

orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins

Mier, Pablo, Andrade-Navarro, Miguel A., Pérez-Pulido, Antonio J., Fernandez-Fuentes, Narcis

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 3.68 MB

english, 2015

42

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

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

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 21.54 MB

english, 2018

43

Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis

Oyama, Linda B., Crochet, Jean-Adrien, Edwards, Joan E., Girdwood, Susan E., Cookson, Alan R., Fernandez-Fuentes, Narcis, Hilpert, Kai, Golyshin, Peter N., Golyshina, Olga V., Privé, Florence, Hess, M

Journal:

Frontiers in Chemistry

Année:

2017

Langue:

english

Fichier:

PDF, 3.78 MB

english, 2017

44

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets

Aguirre-Plans, Joaquim, Piñero, Janet, Sanz, Ferran, Furlong, Laura I., Fernandez-Fuentes, Narcis, Oliva, Baldo, Guney, Emre

Journal:

Journal of Molecular Biology

Année:

2019

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2019

45

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

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

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2019

46

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of ProteinâProtein Interaction Data

Mirela-Bota, Patricia, Aguirre-Plans, Joaquim, Meseguer, Alberto, Galletti, Cristiano, Segura, Joan, Planas-Iglesias, Joan, Garcia-Garcia, Javi, Guney, Emre, Oliva, Baldo, Fernandez-Fuentes, Narcis

Journal:

Journal of Molecular Biology

Année:

2020

Fichier:

PDF, 4.33 MB

2020

47

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

Meseguer, Alberto, Ãrman, Filip, Fornes, Oriol, Molina-FernÃ¡ndez, Ruben, Bonet, Jaume, Fernandez-Fuentes, Narcis, Oliva, Baldo

Journal:

NAR Genomics and Bioinformatics

Année:

2020

Fichier:

PDF, 4.70 MB

2020

48

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

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

Journal:

Frontiers in Plant Science

Année:

2020

Fichier:

PDF, 1.75 MB

2020

49

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

Worthington, Margaret, Perez, Juan Guillermo, Mussurova, Saule, Silva-Cordoba, Alexander, Castiblanco, Valheria, Cardoso Arango, Juan Andres, Jones, Charlotte, Fernandez-Fuentes, Narcis, Skot, Leif, D

Journal:

Journal of Experimental Botany

Année:

2020

Fichier:

PDF, 1.65 MB

2020