• BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data 

      Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra Fontal, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres Viñals, Jordi; Goñi, Ramon; Orozco, Modesto; Gelpí, Josep Lluís (2016-01-04)
      Article
      Accés obert
      Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories ...
    • Genome-wide analysis of the emigrant family of MITEs: amplification dynamics and evolution of genes in Arabidopsis thaliana 

      Santiago, Néstor; Herráiz, Cristina; Messeguer Peypoch, Xavier; Goñi, Ramon; Casacuberta, Josep Maria (2002-01)
      Report de recerca
      Accés obert
      MITEs are structurally similar to defective class II elements but their high copy number and the size and sequence conservation of most MITE families suggest that they can be amplified by a replicative mechanism. Here ...
    • PARMBSC1: A refined force-field for DNA simulations 

      Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balanceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluís; González, Carlos; Vendruscolo, Michele; Laughton, Charles A.; Harris, Sarah A.; Case, David A.; Orozco, Modesto (Nature Publishing Group, 2015-11-16)
      Article
      Accés obert
      We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ~140 μs) ...