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Items: 1 to 50 of 52

1.

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

Fradera-Sola A, Thomas A, Gasior D, Harper J, Hegarty M, Armstead I, Fernandez-Fuentes N.

PLoS One. 2019 Jul 30;14(7):e0220518. doi: 10.1371/journal.pone.0220518. eCollection 2019.

2.

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

Aguirre-Plans J, Piñero J, Sanz F, Furlong LI, Fernandez-Fuentes N, Oliva B, Guney E.

J Mol Biol. 2019 Jun 14;431(13):2477-2484. doi: 10.1016/j.jmb.2019.02.027. Epub 2019 Mar 7.

PMID:
30851278
3.

Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits.

Harper J, De Vega J, Swain S, Heavens D, Gasior D, Thomas A, Evans C, Lovatt A, Lister S, Thorogood D, Skøt L, Hegarty M, Blackmore T, Kudrna D, Byrne S, Asp T, Powell W, Fernandez-Fuentes N, Armstead I.

Ann Bot. 2019 Jun 24;123(6):977-992. doi: 10.1093/aob/mcy230.

4.

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

Sharma P, Lioutas A, Fernandez-Fuentes N, Quilez J, Carbonell-Caballero J, Wright RHG, Di Vona C, Le Dily F, Schüller R, Eick D, Oliva B, Beato M.

Mol Cell. 2019 Jan 3;73(1):84-96.e7. doi: 10.1016/j.molcel.2018.10.016. Epub 2018 Nov 21.

PMID:
30472187
5.

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

Quevedo CE, Cruz-Migoni A, Bery N, Miller A, Tanaka T, Petch D, Bataille CJR, Lee LYW, Fallon PS, Tulmin H, Ehebauer MT, Fernandez-Fuentes N, Russell AJ, Carr SB, Phillips SEV, Rabbitts TH.

Nat Commun. 2018 Aug 9;9(1):3169. doi: 10.1038/s41467-018-05707-2.

6.

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

Geyer KK, Munshi SE, Whiteland HL, Fernandez-Fuentes N, Phillips DW, Hoffmann KF.

PLoS Pathog. 2018 Jun 28;14(6):e1007107. doi: 10.1371/journal.ppat.1007107. eCollection 2018 Jun.

7.

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

Somani A, Smith D, Hegarty M, Fernandez-Fuentes N, Ravella SR, Gallagher JA, Bryant DN.

Genome Announc. 2018 Feb 15;6(7). pii: e01594-17. doi: 10.1128/genomeA.01594-17.

8.

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

Oyama LB, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Privé F, Vallin HE, Wilkinson TJ, Golyshin PN, Golyshina OV, Mikut R, Hilpert K, Richards J, Wootton M, Edwards JE, Maresca M, Perrier J, Lundy FT, Luo Y, Zhou M, Hess M, Mantovani HC, Creevey CJ, Huws SA.

NPJ Biofilms Microbiomes. 2017 Dec 1;3:33. doi: 10.1038/s41522-017-0042-1. eCollection 2017.

9.

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

Marín-López MA, Planas-Iglesias J, Aguirre-Plans J, Bonet J, Garcia-Garcia J, Fernandez-Fuentes N, Oliva B.

Bioinformatics. 2018 Feb 15;34(4):592-598. doi: 10.1093/bioinformatics/btx616.

10.

Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis.

Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA.

Front Chem. 2017 Jul 12;5:51. doi: 10.3389/fchem.2017.00051. eCollection 2017.

11.

Genetic and functional characterization of disease associations explains comorbidity.

Rubio-Perez C, Guney E, Aguilar D, Piñero J, Garcia-Garcia J, Iadarola B, Sanz F, Fernandez-Fuentes N, Furlong LI, Oliva B.

Sci Rep. 2017 Jul 24;7(1):6207. doi: 10.1038/s41598-017-04939-4.

12.

iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments.

Garcia-Garcia J, Valls-Comamala V, Guney E, Andreu D, Muñoz FJ, Fernandez-Fuentes N, Oliva B.

J Mol Biol. 2017 Feb 3;429(3):382-389. doi: 10.1016/j.jmb.2016.11.034. Epub 2016 Dec 10.

PMID:
27956148
13.

Insight into the machinery that oils chromatin dynamics.

Wright RH, Fernandez-Fuentes N, Oliva B, Beato M.

Nucleus. 2016 Nov;7(6):532-539. doi: 10.1080/19491034.2016.1255392. Epub 2016 Nov 28. Review.

14.

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

Kara A, Vickers M, Swain M, Whitworth DE, Fernandez-Fuentes N.

Bioinformatics. 2016 Nov 1;32(21):3339-3341. Epub 2016 Jul 4.

PMID:
27378293
15.

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

Bouraoui H, Desrousseaux ML, Ioannou E, Alvira P, Manaï M, Rémond C, Dumon C, Fernandez-Fuentes N, O'Donohue MJ.

Biotechnol Biofuels. 2016 Jul 8;9:140. doi: 10.1186/s13068-016-0550-x. eCollection 2016.

16.

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

Poglayen D, Marín-López MA, Bonet J, Fornes O, Garcia-Garcia J, Planas-Iglesias J, Segura J, Oliva B, Fernandez-Fuentes N.

Biochem Soc Trans. 2016 Jun 15;44(3):917-24. doi: 10.1042/BST20150001. Review.

PMID:
27284060
17.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

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.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

18.

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

Kara A, Vickers M, Swain M, Whitworth DE, Fernandez-Fuentes N.

BMC Bioinformatics. 2015 Sep 18;16:297. doi: 10.1186/s12859-015-0741-7.

19.

Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment.

Chalmers IW, Fitzsimmons CM, Brown M, Pierrot C, Jones FM, Wawrzyniak JM, Fernandez-Fuentes N, Tukahebwa EM, Dunne DW, Khalife J, Hoffmann KF.

PLoS Negl Trop Dis. 2015 Jul 6;9(7):e0003920. doi: 10.1371/journal.pntd.0003920. eCollection 2015.

20.

VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.

Segura J, Marín-López MA, Jones PF, Oliva B, Fernandez-Fuentes N.

PLoS One. 2015 Mar 12;10(3):e0118107. doi: 10.1371/journal.pone.0118107. eCollection 2015.

21.

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

Oliva B, Fernandez-Fuentes N.

Bioinformatics. 2015 May 1;31(9):1405-10. doi: 10.1093/bioinformatics/btu838. Epub 2014 Dec 23.

PMID:
25540186
22.

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

Bonet J, Segura J, Planas-Iglesias J, Oliva B, Fernandez-Fuentes N.

Bioinformatics. 2014 Jul 1;30(13):1935-6. doi: 10.1093/bioinformatics/btu129. Epub 2014 Mar 6.

PMID:
24603983
23.

Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex.

Sewell H, Tanaka T, El Omari K, Mancini EJ, Cruz A, Fernandez-Fuentes N, Chambers J, Rabbitts TH.

Sci Rep. 2014 Jan 10;4:3643. doi: 10.1038/srep03643.

24.

ArchDB 2014: structural classification of loops in proteins.

Bonet J, Planas-Iglesias J, Garcia-Garcia J, Marín-López MA, Fernandez-Fuentes N, Oliva B.

Nucleic Acids Res. 2014 Jan;42(Database issue):D315-9. doi: 10.1093/nar/gkt1189. Epub 2013 Nov 21.

25.

A modular perspective of protein structures: application to fragment based loop modeling.

Fernandez-Fuentes N, Fiser A.

Methods Mol Biol. 2013;932:141-58. doi: 10.1007/978-1-62703-065-6_9.

26.

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

Segura J, Jones PF, Fernandez-Fuentes N.

Bioinformatics. 2012 Jul 15;28(14):1845-50. doi: 10.1093/bioinformatics/bts269. Epub 2012 May 4.

PMID:
22563069
27.

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

Khan K, Logan CV, McKibbin M, Sheridan E, Elçioglu NH, Yenice O, Parry DA, Fernandez-Fuentes N, Abdelhamed ZI, Al-Maskari A, Poulter JA, Mohamed MD, Carr IM, Morgan JE, Jafri H, Raashid Y, Taylor GR, Johnson CA, Inglehearn CF, Toomes C, Ali M.

Hum Mol Genet. 2012 Feb 15;21(4):776-83. doi: 10.1093/hmg/ddr509. Epub 2011 Nov 7.

28.

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

Segura J, Oliva B, Fernandez-Fuentes N.

Nucleic Acids Res. 2012 Jan;40(Database issue):D479-85. doi: 10.1093/nar/gkr879. Epub 2011 Oct 22.

29.

Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucoma.

Khan K, Rudkin A, Parry DA, Burdon KP, McKibbin M, Logan CV, Abdelhamed ZI, Muecke JS, Fernandez-Fuentes N, Laurie KJ, Shires M, Fogarty R, Carr IM, Poulter JA, Morgan JE, Mohamed MD, Jafri H, Raashid Y, Meng N, Piseth H, Toomes C, Casson RJ, Taylor GR, Hammerton M, Sheridan E, Johnson CA, Inglehearn CF, Craig JE, Ali M.

Am J Hum Genet. 2011 Sep 9;89(3):464-73. doi: 10.1016/j.ajhg.2011.08.005.

30.

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

Segura J, Jones PF, Fernandez-Fuentes N.

BMC Bioinformatics. 2011 Aug 23;12:352. doi: 10.1186/1471-2105-12-352.

31.

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

Segura J, Fernandez-Fuentes N.

Nucleic Acids Res. 2011 Jan;39(Database issue):D755-60. doi: 10.1093/nar/gkq1068. Epub 2010 Nov 18.

32.

Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfaces.

Segura Mora J, Assi SA, Fernandez-Fuentes N.

PLoS One. 2010 Aug 23;5(8):e12352. doi: 10.1371/journal.pone.0012352.

33.

Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma.

Ali M, Buentello-Volante B, McKibbin M, Rocha-Medina JA, Fernandez-Fuentes N, Koga-Nakamura W, Ashiq A, Khan K, Booth AP, Williams G, Raashid Y, Jafri H, Rice A, Inglehearn CF, Zenteno JC.

Mol Vis. 2010 Jun 23;16:1162-8.

34.

A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy.

Ashrafian H, Docherty L, Leo V, Towlson C, Neilan M, Steeples V, Lygate CA, Hough T, Townsend S, Williams D, Wells S, Norris D, Glyn-Jones S, Land J, Barbaric I, Lalanne Z, Denny P, Szumska D, Bhattacharya S, Griffin JL, Hargreaves I, Fernandez-Fuentes N, Cheeseman M, Watkins H, Dear TN.

PLoS Genet. 2010 Jun 24;6(6):e1001000. doi: 10.1371/journal.pgen.1001000.

35.

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

Bowers SR, Calero-Nieto FJ, Valeaux S, Fernandez-Fuentes N, Cockerill PN.

Nucleic Acids Res. 2010 Oct;38(18):6124-34. doi: 10.1093/nar/gkq356. Epub 2010 May 18.

36.

Structural characteristics of novel protein folds.

Fernandez-Fuentes N, Dybas JM, Fiser A.

PLoS Comput Biol. 2010 Apr 22;6(4):e1000750. doi: 10.1371/journal.pcbi.1000750.

37.

Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).

Hermoso A, Espadaler J, Enrique Querol E, Aviles FX, Sternberg MJ, Oliva B, Fernandez-Fuentes N.

Bioinform Biol Insights. 2009 Nov 24;1:77-90.

38.

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces.

Assi SA, Tanaka T, Rabbitts TH, Fernandez-Fuentes N.

Nucleic Acids Res. 2010 Apr;38(6):e86. doi: 10.1093/nar/gkp1158. Epub 2009 Dec 11.

39.

Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita.

Grozdanov PN, Fernandez-Fuentes N, Fiser A, Meier UT.

Hum Mol Genet. 2009 Dec 1;18(23):4546-51. doi: 10.1093/hmg/ddp416. Epub 2009 Sep 4.

40.

Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

Blakaj DM, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, Burk RD, Brenowitz M.

Front Biosci (Landmark Ed). 2009 Jan 1;14:900-17. Review.

41.
42.

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

Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A.

Bioinformatics. 2007 Oct 1;23(19):2558-65. Epub 2007 Sep 6.

PMID:
17823132
43.

M4T: a comparative protein structure modeling server.

Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W363-8. Epub 2007 May 21.

44.

The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen.

Torres M, Fernández-Fuentes N, Fiser A, Casadevall A.

J Biol Chem. 2007 May 4;282(18):13917-27. Epub 2007 Mar 12.

45.

ArchPRED: a template based loop structure prediction server.

Fernandez-Fuentes N, Zhai J, Fiser A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W173-6.

46.

Saturating representation of loop conformational fragments in structure databanks.

Fernandez-Fuentes N, Fiser A.

BMC Struct Biol. 2006 Jul 4;6:15.

47.

Insights into the mechanism of microtubule stabilization by Taxol.

Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, Horwitz SB, Orr GA.

Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10166-10173. doi: 10.1073/pnas.0603704103. Epub 2006 Jun 26.

48.

A supersecondary structure library and search algorithm for modeling loops in protein structures.

Fernandez-Fuentes N, Oliva B, Fiser A.

Nucleic Acids Res. 2006 Apr 14;34(7):2085-97. Print 2006.

49.

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

Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B.

Proteins. 2005 Sep 1;60(4):746-57.

PMID:
16021623
50.

Classification of common functional loops of kinase super-families.

Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B.

Proteins. 2004 Aug 15;56(3):539-55.

PMID:
15229886

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