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; 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 ...
  • 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 ...
  • Challenges of docking in large, flexible and promiscuous binding sites 

    Kotev, Martin; Soliva, Robert; Orozco, Modesto (Elsevier, 2016-10-15)
    Article
    Open Access
    After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; ...
  • Computational Prediction of HIV-1 Resistance to Protease Inhibitors 

    Hosseini, Ali; Alibés, Andreu; Noguera-Julian, Marc; Gil, Victor; Paredes, Roger; Soliva, Robert; Orozco, Modesto; Guallar, Víctor (American Chemical Society, 2016-04-15)
    Article
    Open Access
    Development of mutations in HIV-1 PR hinders the activity of antiretroviral drugs, forcing changes in drug prescription. Most resistance assessments used to date rely on expert-based rules on predefined sets of stereotypical ...
  • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer 

    Heyn, Holger; Vidal, Enrique; Ferreira, Humberto J.; Vizoso, Miguel; Sayols, Sergi; Gomez, Antonio; Moran, Sebastian; Boque-Sastre, Raquel; Guil, Sonia; Martinez-Cardus, Anna; Lin, Charles Y.; Romina, Royo; Sanchez-Mut, Jose V.; Martinez, Ramon; Gut, Marta; Torrents, David; Orozco, Modesto; Gut, Ivo; Young, Richard A.; Esteller, Manel (BioMed Central, 2016-01-26)
    Article
    Open Access
    Background One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. ...
  • Inhibition of Human Enhancer of Zeste Homolog 2 (EZH2) with Tambjamine Analogs 

    Kotev, Martin; Manuel-Manresa, Pilar; Hernando, Elsa; Soto-Cerrato, Vanessa; Orozco, Modesto; Quesada, Roberto; Pérez-Tomás, Ricardo; Guallar, Victor (American Chemical Society, 2017-08-01)
    Article
    Open Access
    Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This ...
  • 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 ...
  • Optimizing a coarse-grained model for the recognition of protein-protein binding 

    Emperador, Agustí; Orozco, Modesto (Barcelona Supercomputing Center, 2015-05-05)
    Conference report
    Open Access
    We are optimizing a force-field to be used with our coarsegrained protein model for the recognition of protein -protein binding. We have found that, apart from ranking correctly the ligand-receptor conformations generated ...
  • 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) ...
  • PMut2: a web-based tool for predicting pathological mutations on proteins 

    López-Ferrando, Victor; Cruz, Xavier de la; Orozco, Modesto; Gelpi, Josep L. (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 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 ...
  • Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression 

    Terrazas, Montserrat; Ivani, Ivan; Villegas, Núria; Paris, Clément; Salvans, Cándida; Brun-Heath, Isabelle; Orozco, Modesto (Oxford University Press (OUP), 2016-05-19)
    Article
    Open Access
    Computational techniques have been used to design a novel class of RNA architecture with expected improved resistance to nuclease degradation, while showing interference RNA activity. The in silico designed structure ...
  • 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, ...
  • 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 ...