Now showing items 21-27 of 27

    • pyDockDNA: a new approach for protein-DNA docking 

      Rodríguez-Lumbreras, Luis Ángel; Jiménez-García, Brian; Fernández-Recio, Juan (Barcelona Supercomputing Center, 2017-05-04)
      Conference report
      Open Access
      Here we present pyDockDNA, which is based on the pyDock program, with a new module for reading and parsing DNA molecules. The protocol is composed of two major steps: sampling and scoring. The first sampling step consists ...
    • pyDockSAXS: protein–protein complex structure by SAXS and computational docking 

      Jiménez-García, Brian; Pons, Carles; Svergun, Dmitri I.; Bernadó, Pau; Fernández-Recio, Juan (Oxford Journals, 2015-07-01)
      Article
      Open Access
      Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques ...
    • SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation 

      Jankauskaite, Justina; Jiménez-García, Brian; Dapkunas, Justas; Fernández-Recio, Juan; Moal, Iain H. (Oxford University Press, 2018-07-18)
      Article
      Open Access
      Motivation: Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the ...
    • Structural and energy determinants in protein-RNA docking 

      Pérez-Cano, Laura; Romero-Durana, Miguel; Fernández-Recio, Juan (Elsevier, 2017-04-15)
      Article
      Open Access
      Deciphering the structural and energetic determinants of protein-RNA interactions harbors the potential to understand key cell processes at molecular level, such as gene expression and regulation. With this purpose, ...
    • Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc 

      Rosell, Albert; Meury, Marcel; Alvarez-Marimon, Elena; Costa, Meritxell; Pérez-Cano, Laura; Zorzano, Antonio; Fernández-Recio, Juan; Palacín, Manuel; Fotiadis, Dimitrios (National Academy of Sciences, 2014-02-25)
      Article
      Open Access
      Heteromeric amino acid transporters (HATs) are the unique example, known in all kingdoms of life, of solute transporters composed of two subunits linked by a conserved disulfide bridge. In metazoans, the heavy subunit is ...
    • Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems 

      Barradas-Bautista, Didier; Rosell, Mireia; Pallara, Chiara; Fernández-Recio, Juan (Academic Press, 2018)
      Part of book or chapter of book
      Open Access
      A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains ...
    • Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2 

      Vreven, Thom; Moal, Iain H.; Vangone, Anna; Pierce, Brian G.; Kastritis, Panagiotis L.; Torchala, Mieczyslaw; Chaleil, Raphael; Jiménez-García, Brian; Bates, Paul A.; Fernández-Recio, Juan; Bonvin, Alexandre M. J. J.; Weng, Zhiping (Elsevier, 2015-09-25)
      Article
      Open Access
      We present an updated and integrated version of our widely used protein–protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein–protein complexes along ...