Now showing items 1-14 of 14

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

      Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codó, Laia; Becerra Fontal, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goni, Ramón; Orozco, Modesto; Gelpí, Josep Lluís (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 ...
    • Cation–π–cation interactions in structural biology 

      Pinheiro, Silvana; Soteras, Ignacio; Gelpí, Josep Lluís; Dehez, François; Chipot, Christophe; Luque, F. Javier; Curutchet, Carles (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      Biological structures are stabilized by a variety of noncovalent interactions, such as hydrogen bonds, π –stacking, salt bridges or hydrophobic interactions. Besides hydrogen bonds and π– stacking, cation–π interactions ...
    • Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking 

      Capella-Gutierrez, Salvador; de la Iglesia, Diana; Haas, Juergen; Lourenco, Analia; Fernandez, José M.; Repchevsky, Dmitry; Dessimoz, Christophe; Schwede, Torsten; Notredame, Cedric; Gelpí, Josep Lluís; Valencia, Alfonso (2017)
      Working paper
      Open Access
      The dependence of life scientists on software has steadily grown in recent years. For many tasks, researchers have to decide which of the available bioinformatics software are more suitable for their specific needs. ...
    • 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 Lluís; 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 Lluís; 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 ...
    • Metadata to describe genomic information 

      Delgado Mercè, Jaime; Naro, Daniel; Llorente Viejo, Silvia; Gelpí, Josep Lluís; Royo, Romina (2018-04)
      Article
      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 ...
    • Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning 

      Diana, Buitrago; Codó, Laia; Illa, Ricard; Jorge, Pau de; Battistini, Federica; Flores, Oscar; Bayarri, Genis; Royo, Romina; Pino, Marc del; Heath, Simon; Hospital, Adam; Gelpí, Josep Lluís; Heath, Isabelle Brun; Orozco, Modesto (Oxford University Press (OUP), 2019-10-10)
      Article
      Open Access
      We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the ...
    • 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
      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) ...
    • PMut2: a web-based tool for predicting pathological mutations on proteins 

      López-Ferrando, Victor; Cruz, Xavier de la; Orozco, Modesto; Gelpí, Josep Lluís (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      Amino acid substitutions in proteins can result in an altered phenotype which might lead to a disease. PMut2 is a method that can predict whether a mutation has a pathological effect on the protein function. It uses current ...
    • 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 Lluís (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 ...
    • Structural and dynamics analysis of pyruvate kinase from erythrocytes: implications in pathology 

      Jordà, Luis; Gelpí, Josep Lluís (Barcelona Supercomputing Center, 2019-05-07)
      Conference report
      Open Access
      Our current study revolves around the dynamic characterization of the human erythrocyte pyruvate kinase (RPYK). The deficiency of this protein is a common cause of nonspherocytic hemolytic anemia, a rare, autosomal ...
    • The Multiple Roles of Waters in Protein Solvation 

      Hospital, Adam; Candotti, Michela; Gelpí, Josep Lluís; 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, ...
    • Web-based tool for the annotation of pathological variants on proteins: PMut 2017 update 

      López-Ferrando​, Víctor; Cruz, Xavier de la; Orozco, Modesto; Gelpí, Josep Lluís (Barcelona Supercomputing Center, 2017-05-04)
      Conference report
      Open Access
      Assessing the impact of amino acid mutations in human health is an important challenge in biomedical research. As sequencing technologies are more available, and more individual genomes become accessible, the number of ...