Publications

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Author Title [ Type(Asc)] Year
Journal
V. Guallar and Wallrapp, F. H., QM/MM methods: looking inside heme proteins biochemistry., Biophysical chemistry, vol. 149, no. 1-2. pp. 1-11, 2010.
V. A. Gil and Guallar, V., pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling., Bioinformatics (Oxford, England), vol. 29, no. 18. pp. 2363-4, 2013.
V. Alejandro Gil and Guallar, V., pyProCT: Automated Cluster Analysis for Structural Bioinformatics, Journal of Chemical Theory and Computation. p. null, 2014.
B. Jiménez-García, Pons, C., and Fernández-Recio, J., pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring., Bioinformatics (Oxford, England), vol. 29, no. 13. pp. 1698-9, 2013.
A. Solernou and Fernández-Recio, J., pyDockCG: new coarse-grained potential for protein-protein docking., The journal of physical chemistry. B, vol. 115, no. 19. pp. 6032-9, 2011.
L. Conde, Vaquerizas, J. M., Ferrer-Costa, C., de la Cruz, X., Orozco, M., and Dopazo, J., PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. Nucleic Acid. Res., 2005.
V. Guallar, Harris, D. L., Batista, V. S., and Miller, W. H., Proton-transfer dynamics in the activation of cytochrome P450eryF., Journal of the American Chemical Society, vol. 124, no. 7. pp. 1430-7, 2002.
T. Meyer, Gabelica, V., Grubmüller, H., and Orozco, M., Proteins in the gas phase. WIRES Comput.Mol.Sci, 2013.
L. Pérez-Cano, Jiménez-García, B., and Fernández-Recio, J., A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data., Proteins, vol. 80, no. 7. pp. 1872-82, 2012.
S. Grosdidier and Fernández-Recio, J., Protein-protein docking and hot-spot prediction for drug discovery., Current pharmaceutical design, vol. 18, no. 30. pp. 4607-18, 2012.
A. N. Naganathan and Orozco, M., The protein folding transition-state ensemble from a Gō-like model., Physical chemistry chemical physics : PCCP, vol. 13, no. 33. pp. 15166-74, 2011.
A. Emperador, Meyer, T., and Orozco, M., Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. Proteins, 78, 83-94, 2009.
E. M. Zdobnov, Campillos, M., Harrington, E. D., Torrents, D., and Bork, P., Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Res, 2005.
A. Duran, Ferrer, R., Ayguadé, E., Badia, R. M., and Labarta, J., A Proposal to Extend the OpenMP Tasking Model with Dependent Tasks. International Journal of Parallel Programming, Volume 37, Issue 3 (2009), pages 292-305, 2009.
A. Barrera-Escoda, Gonçalves, M., Guerreiro, D., Cunillera, J., and Baldasano, J. M., Projections of temperature and precipitation extremes in the North Western Mediterranean Basin by dynamical downscaling of climate scenarios at high resolution (1971–2050), Climatic Change, vol. 122, no. 4. Springer Netherlands, NETHERLANDS, pp. 567-582, 2014.
F. Casagrande, Ratera, M., Schenk, A. D., Chami, M., Valencia, E., López, J. M., Torrents, D., Engel, A., Palacín, M., and Fotiadis, D., Projection structure of a member of the amino acid/polyamine/organocation transporter superfamily.. J Biol Chem. 283(48):33240-8. Epub 2008 Sep 25., 2008.
R. M. Badia, Labarta, J., Sirvent, R., Pérez, J. M., Cela, J. M., and Grima, R., Programming Grid Applications with GRID superscalar. Journal of GRID Computing, 2003.
V. Subotic, Brinkmann, S., Marjanovic, V., Badia, R. M., Gracia, J., Niethammer, C., Ayguadé, E., Labarta, J., and Valero, M., Programmability and portability for exascale: Top down programming methodology and tools with StarSs, Journal of Computational Science, vol. 4. pp. 450–456, 2013.
D. Talavera, Hospital, A., Orozco, M., and de la Cruz, X., A Procedure for the identification of homologous alternative splicing events. BMC. Bioinformatics, 8, 260-271, 2007.
F. Cazorla, Pajuelo, A., Santana, O. J., Fernandez, E., and Valero, M., On the Problem of Evaluating the Performance of Multiprogrammed Workloads. , IEEE Transactions on Computers, vol. 59, no. 12. IEEE, 2010.
F. J. Cazorla, Quiñones, E., Vardanega, T., Cucu, L., Triquet, B., Bernat, G., Berger, E., Abella, J., Wartel, F., Houston, M., Santinelli, L., Kosmidis, L., Lo, C., and Maxim, D., PROARTIS: Probabilistically Analyzable Real-Time Systems, ACM Trans. Embed. Comput. Syst., vol. 12. ACM, New York, NY, USA, pp. 94:1–94:26, 2013.
F. J. Cazorla, Quiñones, E., Vardanega, T., Cucu-Grosjean, L., Triquet, B., Berger, E. D., Abella, J., Wartel, F., Houston, M., Santinelli, L., Kosmidis, L., Lo, C., and Maxim, D., PROARTIS: Probabilistically Analysable Real-Time Systems, ACM Transactions on Embedded Computing Systems. 2012.
F. Cazorla, Quiñones, E., Vardanega, T., Cucu, L., Triquet, B., Bernat, G., Berger, E., Abella, J., Wartel, F., Houston, M., Santinelli, L., Kosmidis, L., Lo, C., and Maxim, D., PROARTIS: Probabilistically Analysable Real-Time Systems, Transactions on Embedded Computing Systems, no. Special Issue on Probabilistic Embedded Computing . ACM, 2012.
C. Guirado, Cuevas, E., Cachorro, V. E., Mimouni, M., Zeudmi, L., Toledano, C., Alonso-Pérez, S., Basart, S., Blarel, L., Goloub, P., and Baldasano, J. M., Preliminary characterization of columnar aerosol properties (AOD-AE) at the Saharan Tamanrasset (Algeria) station, Journal Óptica Pura y Aplicada, vol. 44, no. 4. SPANISH OPTICAL SOCIETY, SPAIN, pp. 635-639, 2011.
C. Pons, Glaser, F., and Fernández-Recio, J., Prediction of protein-binding areas by small-world residue networks and application to docking., BMC bioinformatics, vol. 12. p. 378, 2011.
J. Fernández-Recio, Prediction of protein binding sites and hot spots, WIREs Comput. Mol. Sci. , vol. 1. pp. 680-698, 2011.
F. Cazorla, Knijnenburg, P., Sakellariou, R., Fernández, E., Ramirez, A., and Valero, M., Predictable Performance in SMT processors: Synergy Between the OS and SMTs, IEEE Transactions on Computers, vol. 55, no. 7. pp. 785-799, 2006.
M. Pericas, Ayguadé, E., Zalamea, J., Llosa, J., and Valero, M., Power and Performace Evaluation of Widened and Clustered VLIW Cores. LNCS, 2005.
O. Jorba, Dabdub, D., Blaszczak-Boxe, C., Pérez, C., Janjic, Z., Baldasano, J. M., Spada, M., Badia, A., and Gonçalves, M., Potential significance of photoexcited NO2 on global air quality with the NMMB/BSC chemical transport model, Journal of Geophysical Research, vol. 117, no. D13301. AMER GEOPHYSICAL UNION, UNITED STATES, pp. 1-16, 2012.
A. Soret, Guevara, M., and Baldasano, J. M., The potential impacts of electric vehicles on air quality in the urban areas of Barcelona and Madrid (Spain), Atmospheric Environment, vol. 99, no. December. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND, pp. 51 - 63, 2014.
F. Guim, Rodero, I., Corbalán, J., and Labarta, J., Portal de Acceso a Recursos HPC en Entornos Grid. Boletín RedIRIS 80, 2007.
F. J. Luque, Dehez,, Chipot, C., and Orozco, M., Polarization effects in molecular interactions. Wiley Interdisciplinary Reviews: Computational Molecular Science, n/a., 2011.
C. Ferrer-Costa, Gelpí, J. L., Zamakola, L., Parrága, I., de la Cruz, X., and Orozco, M., PMUT: A Web-based tool for the annotation of pathological mutations on proteins. Bioinformatics, 2005.
T. Hussain, Haider, A., and Ayguadé, E., PMSS: A programmable memory system and scheduler for complex memory patterns, Journal of Parallel and Distributed Computing, vol. 74. pp. 2983–2993, 2014.
T. Hussain, Haider, A., and Ayguadé, E., PMSS: A programmable memory system and scheduler for complex memory patterns, Journal of Parallel and Distributed Computing, vol. 74. pp. 2983–2993, 2014.
A. Queralt and Teniente, E., A platform independent model for the electronic marketplace domain, Software and System Modeling, vol. 7. pp. 219-235, 2008.
O. Deniz, Flores, O., Battistini, F., Pérez, A., Soler-López, M., and Orozco, M., Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., BMC genomics, vol. 12. p. 489, 2011.
Q. Liu, Jiménez, V., Moreto, M., Abella, J., Cazorla, F. J., and Valero, M., Per-task Energy Accounting in Computing Systems, IEEE Computer Architecture Letters, vol. 13. pp. 85–88, 2014.
Q. Liu, Jimenez, V., Moreto, M., Abella, J., Francisco,, and Cazorla, F. J., Per-task Energy Accounting in Computing Systems, In IEEE Computer Architecture Letters (CAL). 2013.
P. Sloot, Talia, D., Reuter, A., Rienhoff, O., Ruter, T., Ullmann, K., Schwiegelshohn, U., Badia, R. M., Bubak, M., Danelutto, M., Dustdar, S., Gagliardi, F., Geiger, A., Hluchy, L., Kranzlmuller, D., Laure, E., Priol, T., Reinefeld, A., and Resch, M., Perspectives on grid computing. Future Generation Computer Systems, Volume 26, Issue 8, October 2010, Pages 1104-1115, 2010.
Z. Pipirou, Guallar, V., Basran, J., Metcalfe, C. L., Murphy, E. J., Bottrill, A. R., Mistry, S. C., and Raven, E. L., Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase., Biochemistry, vol. 48, no. 16. pp. 3593-9, 2009.
V. Guallar, Baik, M. - H., Lippard, S. J., and Friesner, R. A., Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450., Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 12. pp. 6998-7002, 2003.
J. Corbalán, Martorell, X., and Labarta, J., Performance-Driven Processor Allocation. IEEE Transactions on Parallel and Distributed Systems, 2005.
T. Morad, Weiser, U., Kolodny, A., Valero, M., and Ayguadé, E., Performance, Power Efficiency and Scalability of Asymmetric Cluster Chip Multiprocessors. IEEE CAL, Computer Architecture Letters, 2006.
I. Soteras, Orozco, M., and Luque, F. J., Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. J.Computer Aided Mol.Design. (2010), 24, 281-291., 2010.
I. Soteras, Forti, F., Orozco, M., and Luque, F. J., Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies. J. Phys. Chem. B, 2009, 113 (27), pp 9330?9334, 2009.
P. Banás, Hollas, D., Zgarbová, M., Jurecka, P., Orozco, M., Cheatham, T. E., Sponer, J., and Otyepka, M., Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 2010, 6 (12), pp 3836?3849, 2010.
A. Klamt, Mennucci, B., Tomasi, J., Barone, V., Curutchet, C., Orozco, M., and Luque, F. J., On the performance of continuum solvation methods. A comment on Universal Approaches to Solvation Modeling. Acc. Chem. Res., 2009, 42 (4), pp 489?492, 2009.
S. Reyes, Muñoz-Caro, C., Niño, A., Badia, R. M., and Cela, J. M., Performance of computation-intensive, parameter sweep applications on Internet-based Grids of computers. The mapping of molecular potential energy hypersurfaces. Concurrency and Computation: Practice and Experience, 2007.
M. Álvarez, Ramirez, A., Valero, M., Azevedo, A., Meenderinck, C., and Juurlink, B., Performance Evaluation of Macroblock-level Parallelization of H.264 Decoding on a cc-NUMA Multiprocessor Architecture, Avances en Sistemas e Informática, vol. 6, no. 1. pp. 219-228, 2009.

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