Now showing items 1-6 of 6

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

    Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codó, Laia; Becerra, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goni, Ramón; Orozco, Modesto; Gelpí, Josep Ll. (Oxford Journals, 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 ...
  • Long-timescale dynamics of the Drew–Dickerson dodecamer 

    Dans, Pablo D.; Danilāne, Linda; Ivani, Ivan; Dršata, Tomáš; Lankaš, Filip; Hospital, Adam; Walther, Jürgen; Illa-Pujagut, Ricard; Battistini, Federica; Gelpí, Josep Ll.; Lavery, Richard; Orozco, Modesto (2016-04-15)
    Article
    Open Access
    We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the ...
  • Metadata to Describe Genomic Information 

    Delgado, Jaime; Naro, Daniel; Llorente, Silvia; Gelpí, Josep Ll.; Royo, Romina (IOS Press, 2018)
    Part of book or chapter of book
    Open Access
    Interoperable metadata is key for the management of genomic information. We propose a flexible approach that we contribute to the standardization by ISO/IEC of a new format for efficient and secure compressed storage and ...
  • 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) ...
  • PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update 

    López-Ferrando, Víctor; Gazzo, Andrea; de la Cruz, Xavier; Orozco, Modesto; Gelpí, Josep Ll. (Oxford University Press, 2017-04-27)
    Article
    Open Access
    We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a ...
  • The Multiple Roles of Waters in Protein Solvation 

    Hospital, Adam; Candotti, Michela; Gelpí, Josep Ll.; Orozco, Modesto (American Chemical Society, 2017-01-06)
    Article
    Open Access
    Extensive molecular dynamics (MD) simulations have been used to characterize the multiple roles of water in solvating different types of proteins under different environmental conditions. We analyzed a small set of proteins, ...