Now showing items 1-3 of 3

  • 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; Gelpi, Josep Lluis (2016-01-04)
    Article
    Open Access
    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)
    External research report
    Open Access
    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 Ll.; González, Carlos; Vendruscolo, Michele; Laughton, Charles A.; Harris, Sarah A.; Case, David A.; Orozco, Modesto (Nature Publishing Group, 2015-11-16)
    Article
    Open Access
    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) ...