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Research and Development

The scientific team of biomol-informatics has broad experience in knowledge translation between bioinformatics simulation and laboratories of research and diagnostics.

Participation in European Projects (FP7):

"DORIAN" consortium : FP7 collaborative project HEALTH-F3-2009-223431 "Developmental Origins of Healthy and Unhealthy Ageing: The Role of Maternal Obesity".  2011-2015. [Download DORIAN flyer -PDF-].


"EpiTRAITS" consortium : FP7 Marie Curie project FP7-PEOPLE-2012-ITN-316965 "Epigenetic regulation of economically important plant traits". 2012-2025


"IMI-ENABLE" consortium, a Innovatives Medicines Initiative within IMI’s New Drugs for Bad Bugs (ND4BB) programme (ref. IMI-DB4BB-ENABLE-115583). 2014-2020.


Coordination of INNPACTO Spanish National Project:

Biomol-Informatics coordinates the "DIGEN-1K" INNPACTO consortium (participants: Madrid Science Park, IdiPaz, CBMSO:CSIC-UAM) financed by the Spanish Plan Nacional I+D+I 2011 (Ref: IPT-2011-0964-900000). 2011-2014.



Finished projects:

"DIVINOCELL" Consortium : FP7 collaborative project FP7-HEALTH-2011-278603 "Exploiting Gram-negative cell division targets in the test tube to obtain antimicrobial compounds".  2009 - 2013.


Activities Program among R&D groups of the Comunidad de Madrid : Program S-BIO-0260/2006 "COMBACT: New targets to combat pathogenic bacteria". 2007-2010



Scientific publications:

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Iozzo, P., Holmes, M., Schmidt, M.V., Cirulli, F., Guzzardi, M.A., Berry, A., Balsevich, G., Andreassi, M.G., Wesselink J.J., Liistro, T. Gómez-Puertas, P., Eriksson, J.G. & Seckl, J. (2014). Developmental ORIgins of Healthy and Unhealthy AgeiNg: The Role of Maternal Obesity - Introduction to DORIAN. Obesity Facts 7, 130-151.  [http://dx.doi.org/10.1159/000362656]
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Mendieta-Moreno, J., Walker, R., Lewis, J., *Gómez-Puertas, P., ^Mendieta, J. & *^Ortega, J. (*Corresponding authors; ^Co-last authors) (2014). FIREBALL/AMBER: An efficient local-orbital DFT QM/MM method for biomolecular systems. Journal of Chemical Theory and Computation, in press.  [http://dx.doi.org/10.1021/ct500033w]
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Betancor, G., ,Nevot, M., Mendieta, J., Gómez-Puertas, P., Martínez, M.A. & Menéndez-Arias, L. (2014). Molecular basis of the association of H208Y and thymidine analogue resistance mutations M41L, L210W and T215Y in the HIV-1 reverse transcriptase of treated patients. Antiviral Research106, 42-52.  [http://dx.doi.org/10.1016/j.antiviral.2014.03.004]
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Gonzalez de Prado Salas, P., Hörger, I., Martín-García, F., Mendieta, J., Alonso, A., Encinar, M., Gómez-Puertas, P., Vélez, M. & Tarazona, P. (2014). Torsion and curvature of FtsZ filaments. Soft Matter 10, 1977-1986.  [http://dx.doi.org/10.1039/c3sm52516c]
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Filipa P Reis, F.P., Barbas, A., Klauer, A.A., Schaeffer, D., López-Viñas, E., Gómez-Puertas, P., van Hoof, A. & Arraiano, C.M. (2013). Modulating the RNA processing and decay by the exosome: altering Rrp44/Dis3 activity and end-product. PLoS ONE 8(11): e76504.  [http://dx.doi.org/10.1371/journal.pone.0076504]
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Rodríguez, J.M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.J., López, G., Valencia, A. & Tress, M. (2013). APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research 41(Database issue), D110-D117.  [http://dx.doi.org/10.1093/nar/gks1058]
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Martín-García, F., Mendieta-Moreno, J.I., Marcos-Alcalde, I, *Gómez-Puertas, P. & Mendieta, J. (* Corresponding author). (2013). Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: An alternative role for ß-Glu 188. Biochemistry 52, 959-966.  [http://dx.doi.org/10.1021/bi301109x]
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Wesselink, J.J., López-Camacho, E., De la Peña, S., Ramos-Ruiz, R., Ruiz-Carrascoso, G., Lusa-Bernal, S., Fernández-Soria, V., Gómez-Gil, R., *Gómez-Puertas, P. & *Mingorance, J. (* Corresponding authors). (2012). Genome sequence of OXA-48 carbapenemase producing Klebsiella pneumoniae KpO3210. Journal of Bacteriology 194, 6981.  [http://dx.doi.org/10.1128/JB.01897-12]
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Perteguer, M.J., Gómez-Puertas, P., Cañavate, C., Dagger, F., Gárate, T. & Valdivieso, E. (2012). Ddi1-like protein from Leishmania major is an active Aspartyl-Proteinase. Cell Stress & Chaperones, in press.  [PubMed]  [http://dx.doi.org/10.1007/s12192-012-0368-9]
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Arnedo, M., Menao, S., Puisac, B., Teresa-Rodrigo, M., Gil-Rodríguez, M., López-Viñas, E., Gómez-Puertas, P., Casals, N., Casale, C.H., Hegardt, F.G. & Pie, J. (2012). Characterization of a novel HMG-CoA Lyase enzyme with a dual location in endoplasmic reticulum and cytosol. Journal of Lipid Research 53, 2046-2056.  [PubMed]  [http://dx.doi.org/10.1194/jlr.M025700]
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González-Magaldi, M., Postigo, R., de la Torre, B.G., Vieira, Y.A, López-Viñas, E., Gómez-Puertas, P., Andreu, D., Kremer, L., Rosas, M.F. & Sobrino, F. (2012). Mutations that hamper dimerization of foot-and-mouth disease virus 3A protein are detrimental for infectivity. Journal of Virology, in press.  [PubMed]  [http://dx.doi.org/10.1128/JVI.00580-12]
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Mendieta, J., Pérez-Lago, L., Salas, M., & Camacho A. (2012). Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove. Journal of Bacteriology 194, 4727-35.  [PubMed]  [http://dx.doi.org/10.1128/JB.00677-12]
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Matos, R.G., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2012). The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes. Biochimica et Biophysica Acta (BBA) - General Subjects 1820, 1543–1552.  [PubMed]  [http://dx.doi.org/10.1016/j.bbagen.2012.06.009]
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Martín-García, F., Salvarelli, E., Mendieta-Moreno, J.I., Vicente, M., Mingorance, J., Mendieta, J. & Gómez-Puertas, P. (2012). Molecular dynamics simulation of GTPase activity in polymers of the cell division protein FtsZ. FEBS Letters 586, 1236–1239.  [PubMed]  [http://dx.doi.org/10.1016/j.febslet.2012.03.042]
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Martín-García, F., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2012). Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion. Biochemical and Biophysical Research Communications 420, 42-47.  [PubMed]  [http://dx.doi.org/10.1016/j.bbrc.2012.02.112]
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Martín-García, F., Mendieta-Moreno, J.I., López-Viñas, E., *Gómez-Puertas, P. & *Mendieta, J. (* Co-last authors) (2012). The Role of Gln(61) in HRas GTP Hydrolysis: A Quantum Mechanics/Molecular Mechanics Study. Biophysical Journal 102, 152-157.  [PubMed]  [http://dx.doi.org/10.1016/j.bpj.2011.11.4005]
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López, E., Wesselink, J.J., López, I., Mendieta, J., *Gómez-Puertas, P. & *Muñoz, S.R. (* Co-last authors) (2011). Technical phosphoproteomic and bioinformatic tools useful in cancer research. Journal of Clinical Bioinformatics 1, 26.  [PubMed]
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Puisac, B., Ramos, M., Arnedo, M., Menao, S., Gil-Rodríguez, M.C., Teresa-Rodrigo, M.E., Pié, A., de Karam, J.C., Wesselink, J.J., Giménez, I., Ramos, F.J., Casals, N., Gómez-Puertas, P., Hegardt, F.G. & Pié, J. (2011). Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway. Molecular Biology Reports 39, 4777-4785.  [PubMed]  [http://dx.doi.org/10.1007/s11033-011-1270-8]
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Kisic, M., Matamoros, T., Nevot, M., Mendieta, J., Martínez-Picado, J., Martínez, M.A. & Menéndez-Arias, L. (2011). Thymidine analogue excision and discrimination modulated by mutational complexes including single amino acid deletions of Asp-67 or Thr-69 in HIV-1 reverse transcriptase. Journal of Biological Chemistry 286, 20615-20624.  [PubMed]
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Matos, R.G., Barbas, A, Gómez-Puertas, P. & Arraiano, C.M. (2011). Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade dsRNA. PROTEINS: Structure, Function, and Bioinformatics 79, 1853-1867.  [PubMed]
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Oroz, J., Valbuena, A., Vera, A.M., Mendieta, J., Gómez-Puertas, P. & Carrión-Vázquez M. (2011). Nanomechanics of the cadherin ectodomain: 'canalization' by Ca2+ binding results in a new mechanical element. Journal of Biological Chemistry; in press.  [PubMed]
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López, E., Matthiesen, R., Mendieta, J., Wesselink, J.J., Gómez-Puertas, P. & Ferreira, A. (2011). Functional phosphoproteomics tools for current immunological disorders research. Journal of Integrated -OMICS. 1, 1-16.  [Journal]
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Hurtado, C., Bustos, M.J., Granja, A.G., de León, P., Sabina, P., López-Vinas, E., Gómez-Puertas, P., Revilla, Y. & Carrascosa, A.L. (2010). The African swine fever virus lectin EP153R modulates the surface membrane expression of MHC class I antigens. Archives of Virology; in press..  [PubMed]
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Mingorance, J., Rivas, G., Vélez, M., Gómez-Puertas, P. & Vicente, M. (2010). Strong FtsZ is with the force: mechanisms to constrict bacteria. Trends in Microbiology. 18, 348-356.  [PubMed]
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Romanelli, V., Belinchón, A., Benito-Sanz, S., Martínez-Glez, V., Gracia-Bouthelier, R., Heath, K.E., Campos-Barros, A., García-Miñaur, S., Fernández, L., Meneses, H., López-Siguero, J.P., Guillén-Navarro, E., Gómez-Puertas, P., Wesselink, J.J., Mercado, G., Esteban-Marfil, V., Palomo, R., Mena, R., Sánchez, A., del Campo, M. & Lapunzina, P. (2010). CDKN1C (p57Kip2) Analysis in Beckwith-Wiedemann syndrome (BWS) Patients: Genotype-Phenotype Correlations, Novel Mutations, and Polymorphisms. American Journal of Medical Genetics Part A. 152A, 1390-1397.  [PubMed]
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Pié, J., Gil-Rodríguez, M.C., Ciero, M., López-Viñas, E., Ribate, M.P., Arnedo, M., Deardorff, M.A., Puisac, B., Legarreta, J., de Karam, J.C., Rubio, E., Bueno, I., Baldellou, A., Calvo, M.T., Casals, N., Olivares, J.L., Losada, A., Hegardt, F.G., Krantz, I.D., Gómez-Puertas, P. & Ramos F.J. (2010). Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. American Journal of Medical Genetics. Part A. 152A, 924-929.  [PubMed]
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Mendieta, J., Rico, A.I., López-Viñas, E., Vicente, M., Mingorance, J. & Gómez-Puertas, P. (2009). Structural and Functional Model for Ionic (K+/Na+) and pH Dependence of GTPase Activity and Polymerization of FtsZ, the Prokaryotic Ortholog of Tubulin. Journal of Molecular Biology 390, 17-25.  [PubMed]
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Barbas, A., Matos, R.G., Amblar, M., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2009). Determination of key residues for catalysis and RNA-cleavage specificity: one mutation turns RNase II into a "super"-enzyme. Journal of Biological Chemistry 284, 20486-20498.  [PubMed]
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Barbas, A., Matos, R.G., Amblar, M., López-Viñas, E., Gómez-Puertas, P. & Arraiano, C.M. (2008). New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end-product. Journal of Biological Chemistry 283, 13070-13076.  [PubMed]
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Llorente, M.T., Taylor, I.A., López-Viñas, E., Gómez-Puertas, P., Calder, L.J., García-Barreno, B. & Melero, J.A. (2008). Structural properties of the human respiratory syncytial virus P protein: Evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase co-factors. PROTEINS: Structure, Function and Bioinformatics 72, 946-958.  [PubMed]
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Asenjo, A., Mendieta, J., Gómez-Puertas, P. & Villanueva, N. (2008). Residues in human Respiratory syncytial virus P protein that are essential for its activity on RNA viral synthesis. Virus Research 132, 160-173.  [PubMed]
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Blas-Galindo, E., Cava, F., López-Viñas, E., Mendieta, J. & Berenguer, J. (2007). Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus. Applied and Environmental Microbiology 73, 5138-5145.  [PubMed]
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Pié J., López-Viñas, E., Puisac, B., Menao, S., Pié A., Casale, C., Ramos, F., Hegardt, F.G., Gómez-Puertas, P. & Casals, N. (2007). Molecular genetics of HMG-CoA lyase deficiency. Molecular Genetics and Metabolism 92, 198-209.  [PubMed
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López-Viñas, E., Bentebibel, A., Gurunathan, C., Morillas, M., De Arriaga, D., Serra, D., Asins, G., Hegardt, F. & Gómez-Puertas, P. (2007). Definition by functional and structural analysis of two malonyl-CoA sites in carnitine palmitoyltransferase 1A. Journal of Biological Chemistry 282, 18212-18224.  [PubMed
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López-Viñas, E.*, Atrian, S.*, Gomez-Puertas, P., Chabás, A., Vilageliu, L. & Grinberg, D. (2007). An evolutionary and structure-based docking model for glucocerebrosidase-saposin C and glucocerebrosidase-substrate interactions. Relevance for Gaucher disease. PROTEINS: Structure, Function and Bioinformatics 70, 882-891.(* Co-first authors)  [PubMed
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Carrasco, P., Menao, S., López-Viñas, E., Santpere, G., Clotet, J., Sierra, A.Y., Gratacos, E., Puisac, B., Gomez-Puertas, P., Hegardt, F.G., Pie, J. & Casals, N. (2007). C-Terminal End and Aminoacid Lys48 in HMG-Coa Lyase Are Involved in Substrate Binding and Enzyme Activity. Molecular Genetics and Metabolism 91, 120-127.  [PubMed]  (cover paper).
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