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February 2017. Congrats to Stefani. Find out more ...
December 2016. One more before the end of the year. Find out more ...
November 2016. New publication. Find out more ...
July 2016. Belated welcome to Alexis. Find out more ...
July 2016. A bumper month. Find out more ...
June 2016. New publication. Find out more ...
June 2016. Updates on Frag'R'Us and ArchPRED libraries. Find out more ...
May 2016. New publication. Find out more ...
 
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Publications
    Publications By Year
    [2017] [2016] [2015] [2014] [2013] [2012] [2011] [2010] [2009]
    [2007] [2006] [2005] [2004] [2002

    2017


  • 50. Linda B. Oyama, Susan E. Girdwood, Alan R. Cookson, Narcis Fernandez-Fuentes, Florence Privé, Hannah E. Vallin, Toby J. Wilkinson, Peter N. Golyshin, Olga V. Golyshina, Ralf Mikut, Kai Hilpert, Jennifer Richards, Mandy Wootton, Joan E. Edwards, Marc Maresca, Josette Perrier, Fionnuala T. Lundy, Yu Luo, Mei Zhou, Matthias Hess, Hilario C. Mantovani, Christopher J. Creevey & Sharon A. Huws. The rumen microbiome: an underexplored resource for novel antimicrobial discovery npj Biofilms and Microbiomes 3: 33 (2017) doi:10.1038/s41522-017-0042-1
  • 49. Manuel Alejandro Marin-Lopez, Joan Planas-Iglesias, Joaquim Aguirre-Plans, Jaume Bonet, Javier Garcia-Garcia, Narcis Fernandez-Fuentes, Baldo Oliva. On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. Bioinformatics. 2017 Sep 27. doi: 10.1093/bioinformatics/btx616. [Epub ahead of print].
  • 48. Carlota Rubio-Perez, Emre Guney, Daniel Aguilar, Janet Piñero, Javier Garcia-Garcia, Barbara Iadarola, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Baldo Oliva. Genetic and functional characterization of disease associations explains comorbidity. Sci Rep. 2017 Jul 24;7(1):6207. doi: 10.1038/s41598-017-04939-4.
  • 47. Linda B. Oyama, Jean-Adrien Crochet, Joan E. Edwards, Susan E. Girdwood, Alan R. Cookson, Narcis Fernandez-Fuentes, Kai Hilpert, Peter N. Golyshin, Olga V. Golyshina, Florence Privé, Matthias Hess, Hilario C. Mantovani, Christopher J. Creevey, Sharon A. Huws. Buwchitin: A ruminal peptide with antimicrobial potential against Enterococcus faecalis. Fronteirs in Chemistry, 5:51. doi: 10.3389/fchem.2017.00051
  • 2016


  • 46. Garcia-Garcia J, Valls-Comamala V, Guney E, Andreu D, Munoz FJ, Fernandez-Fuentes N, Oliva B. iFraG: A protein-protein interface prediction server based on sequence fragments. Journal of Molecular Biolgy. 2016 Dec 9. ppii: S0022-2836(16)20532-9 [Epub ahead of print], doi:10.1016/j.jmb.2016.11.034
  • 45. Roni GH Wright, Narcis Fernandez-Fuentes N, Baldo Oliva, Miguel Beato. Insight into the machinery that oils chromatin dynamics. Nucleus. 016 Nov 28:1-8. [Epub ahead of print], doi:10.1080/19491034.2016.1255392
  • 44. Bouraoui H, Desrousseaux ML, Ioannou E, Alvira P, Manaï M, Rémond C, Dumon C, Fernandez-Fuentes N, O'Donohue MJ. The GH51 α-l-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans. Biotechnol Biofuels. 2016 Jul 8;9:140. doi:10.1186/s13068-016-0550-x.
  • 43. Altan Kara, Martin Vickers, Martin Swain, David E. Whitworth and Narcis Fernandez-Fuentes MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins. Bioinformatics. 2016 Jul 4. pii: btw403. [Epub ahead of print]
  • 42. Daniel Poglayen, Manuel Alejandro Marín-López, Jaume Bonet, Oriol Fornes, Javier Garcia-Garcia, Joan Planas-Iglesias, Joan Segura, Baldo Oliva, Narcis Fernandez-Fuentes InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research. Biochemical Society Transations. 2016 Jun 15;44(3):917-24. doi: 10.1042/BST20150001.
  • 41. Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. 2016 Apr 28. doi:10.1002/prot.25007. [Epub ahead of print]
  • 2015


  • 40. Altan Kara, Martin Vickers, Martin Swain, David E Whitworth and Narcis Fernandez-Fuentes. Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. BMC Bioinformatics. 2015
  • 39. Iain W. Chalmers, Colin M. Fitzsimmons, Martha Brown, Christine Pierrot, Frances M. Jones, Jakub M. Wawrzyniak, Narcis Fernandez-Fuentes, Edridah M. Tukahebwa, David W. Dunne, Jamal Khalife, Karl F. Hoffmann. Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment. PLoS Neglected Tropical Diseases. 2015
  • 38. Joan Segura, Manuel-Alejandro Marin-Lopez, Pamela F Jones, Baldomero Oliva and Narcis Fernandez-Fuentes. VORFFIP-Driven Dock: V-D²OCK, a Fast and Accurate Protein Docking Strategy. PLoS One. 2015
  • 37. Baldomero Oliva and Narcis Fernandez-Fuentes. Knowledge-based modeling of peptides at protein interfaces: PiPreD. Bioinformatics. 2015
  • 2014


  • 36. Jaume Bonet, Andras Fiser, Baldomero Oliva, Narcis Fernandez-Fuentes. Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications Bio-Algorithms and Med-Systems (2014)
  • 35. Jaume Bonet, Joan Segura, Joan Planas-Iglesias, Baldomero Oliva, Narcis Fernandez-Fuentes. Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design Bioinformatics. 2014
  • 34. Helen Sewell, Tomo Tanaka, K. El Omari, Erika J Mancine, A. Cruz, Narcis Fernandez-Fuentes, Jennifer Chambers and Terence H Rabbitts. Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex Scientific Reports. 2014
  • 33. Jaume Bonet, Joan Planas-Iglesias, J Garcia-Garcia, MA Marin-Lopez, Narcis Fernandez-Fuentes and Baldo Oliva. ArchDB 2014: structural classification of loops in proteins Nucleic Acids Research. 2014
  • 2013


  • 32. A. Cruz-Migoni, Narcis Fernandez-Fuentes and Terence H Rabbitts. Peptides: minimal drug surrogates to interrogate and interfere with protein function Medicinal Chemistry Communications. 2013
  • 31. Narcis Fernandez-Fuentes and Andras Fiser. A Modular Perspective of Protein Structures: Application to Fragment Based Loop Modeling Methods in Molecular Biology. 2013
  • 2012


  • 30. Joan Segura, Pamela F Jones and Narcis Fernandez-Fuentes. A holistic in silico approach to predict functional sites in protein structures Bioinformatics. 2012
  • 29. Jose Ramon Blas Pastor, Joan Segura, Narcis Fernandez-Fuentes. Computational Tools and Databases for the Study and Characterization of Protein Interactions. Protein-Protein Interactions - Computational and Experimental Tools, ISBN: 978-953-51-0397-4
  • 2011


  • 28. Kamron Khan, Clare V. Logan1, Martin McKibbin, Eamonn Sheridan, Nursel H. Elçioglu, Ozlem Yenice, David A. Parry, Narcis Fernandez-Fuentes, Zakia I.A. Abdelhamed, Ahmed Al-Maskari, James A. Poulter, Moin D. Mohamed, Ian M. Carr, Joanne E. Morgan, Hussain Jafri, Yasmin Raashid, Graham R. Taylor, Colin A. Johnson, Chris F. Inglehearn, Carmel Toomes, and Manir Ali. Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defects. Human Molecular Genetics. 2011
  • 27. Joan Segura, Baldo Oliva and Narcis Fernandez-Fuentes. CAPS-DB: a structural classification of helix-capping motifs. Nucleic Acids Research. 2011
  • 26. 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 Fogarty, Ian M. Carr, James A. Poulter, Joanne E. Morgan, Moin D. Mohamed, Hussain Jafri, Yasmin Raashid, Ngy Meng, Horm Piseth, Carmel Toomes, Robert J. Casson, Graham R. Taylor, Michael Hammerton, Eamonn Sheridan, Colin A. Johnson, Chris F. Inglehearn, Jamie E. Craig, Manir Ali. Homozygous Mutations in PXDN Cause Congenital Cataract, Corneal Opacity, and Developmental Glaucoma. AJHM. 2011
  • 25. Joan Segura Mora, Pamela F Jones and Narcis Fernandez-Fuentes. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi Diagrams (VORFFIP). BMC Bioinformatics. 2011
  • 24. Joan Segura Mora and Narcis Fernandez-Fuentes. PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. Nucleic Acids Research. 2011.
  • 2010


  • 23. Joan Segura Mora, Salam A. Assi, Narcis Fernandez-Fuentes. Presaging Critical Residues in Protein interfaces-Web server (PCRPi-W): a web server to chart hot spot in protein interfaces. PlOS One. 2010.
  • 22. Manir Ali, Beatriz Buentello-Volante, Martin McKibbin, J. Alberto Rocha-Medina, Narcis Fernandez-Fuentes, Wilson Koga-Nakamura, Aruna Ashiq, Kamron Khan,Adam P. Booth, Yasmin Raashid, Hussain Jafri, Aine Rice, Chris F. Inglehearn, Juan Carlos Zenteno. Homozygous FoxE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma. Molecular Vision. 2010.
  • 21. Houman Ashrafian, Louise Docherty, Vincenzo Leo, Christopher Towlson, Monica Neilan, Violetta Steeples, Craig A. Lygate, Tertius Hough, Stuart Townsend, Debbie Williams, Sara Wells, Dominic Norris, Sarah Glyn-Jones, John Land, Ivana Barbaric, Zuzanne Lalanne, Paul Denny, Dorota Szumska, Shoumo Bhattacharya, Julian L. Griffin, Iain Hargreaves, Narcis Fernandez-Fuentes, Michael Cheeseman, Hugh Watkins, T. Neil Dear. A mutation in the mitochondrial fission gene Dnm1l leads to cardomyopathy. PlOS Genetics. 2010.
  • 20. Sarion R. Bowers, Fernando J. Calero-Nieto, Stephanie Valeaux, Narcis Fernandez-Fuentes, and Peter N. Cockerill. Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer. Nucleic Acid Research. 2010.
  • 19. N. Fernandez-Fuentes, J. Dybas, A. Fiser. Structural characteristics of novel protein folds. PLoS Computational Biology. 2010.
  • 2009


  • 18. N. Fernandez-Fuentes, A. Fiser. Modeling loops in protein structures. In Protein Structure Prediction: Method and Algorithms. Wiley Book Series on Bioinformatics.
  • 17. S.A. Assi, T. Tanaka, T.H. Rabbitts, N. Fernandez-Fuentes. PCRPi: Presaging Critical Residues in Protein interface, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Research. 2009.
  • 16. P.N. Grozdanov, N. Fernandez-Fuentes, A. Fiser, U.T. Meier. Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita. Human Mol. Genetics. 2009
  • 15. D.M. Blakaj, N. Fernandez-Fuentes, Z. Chen, R. Hegde, A. Fiser, R.D. Burk, M. Brenowitz. Evolutionary and biophysical relationships among the papillomavirus E2 proteins. Frontiers in Bioscience. 2009
  • 2007


  • 14. A. Hermoso, J. Espadaler, E. Querol, F.X. Aviles, M.J.E. Sternberg, B. Oliva, N. Fernandez-Fuentes. ArchDB: Including Functional Annotations and Expanding the Database of Classified Structural Motifs. Bioinformatics and Biology Insights. 2007
  • 13. M. Torres, N. Fernandez-Fuentes, A. Fiser, A. Casadevall. Heterologous constant chains impart kinetic and thermodynamic differences in antigen binding for immunoglobulins with identical variable-regions. PlOS ONE. 2007
  • 12. N. Fernandez-Fuentes, B.K. Rai, C.J. Madrid-Aliste, J.E. Fajardo, A. Fiser. Comparative protein structure modeling by combining of multiple templates and optimizing sequence-to-structure alignments. Bioinformatics. 2007
  • 11. N. Fernandez-Fuentes, B.K. Rai, C.J. Madrid-Aliste, J.E. Fajardo, A. Fiser. M4T: a comparative protein structure modeling server. Nucleic Acids Research. 2007
  • 10. M. Torres, N. Fernandez-Fuentes, A. Fiser, A. Casadevall. The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen. J.B.C. 2007
  • 2006


  • 9. N. Fernandez-Fuentes, H. Xiao, P. Verdier-Pinar, B. Burd, R. Angeletti, A. Fiser, S.B. Horwitz, G. Orr. Insights into the mechanism of microtubule stabilization by Taxol. PNAS. 2006
  • 8. N. Fernandez-Fuentes and A. Fiser. Saturating representation of conformational fragments in structure databanks. BMC Structural Biology. 2006
  • 7. N. Fernandez-Fuentes, J. Zhai and A. Fiser. ArchPred: a template based loop structure prediction server. Nucleic Acids Research. 2006
  • 6. N. Fernandez-Fuentes, B. Oliva, A. Fiser. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Research. 2006
  • 2005


  • 5. N. Fernandez-Fuentes, E. Querol, F.X. Aviles, M.J.E. Sternberg, B. Oliva. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins: Structure, Function, and Bioinformatics. 2005
  • 2004


  • 4. N. Fernandez-Fuentes, A. Hermoso, J. Espadaler, E. Querol, F.X. Aviles, B. Oliva. Classification of common functional loops of super-families of kinases. Proteins: Structure, Function, and Bioinformatics. 2004
  • 3. J. Espadaler, N. Fernandez-Fuentes, A. Hermoso, E. Querol, F.X. Aviles, M.J.E. Sternberg, B. Oliva. ArchDB: Automated protein loop classification as a tool for Structural Genomic. Nucleic Acids Research. 2004
  • 2002


  • 2. J. Espadaler, N. Fernandez-Fuentes, E. Querol, F.X. Aviles, M.J.E. Sternberg, and B. Oliva. Updated protein loop classification: Improving the automatic class partition and finding of functional 3D motifs. J.B.I. 2002
  • 1. S. Dietmann, N. Fernandez-Fuentes, L. Holm. Automated detection of remote homology. Current Opinion in Structural Biology. 2002