Browsing by Author "Orozco, Modesto"

Now showing items 1-19 of 19

    • A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort 

      Beltran, Daniel; Hospital, Adam; Gelpi, Josep; Orozco, Modesto (Oxford University Press, 2023-11)
      Article
      Open Access
      Abstract Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety ...

    • 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 Viñals, 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 ...

    • BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools 

      Bayarri, Genís; Andrio, Pau; Hospital, Adam; Orozco, Modesto; Gelpi, Josep (Oxford University Press, 2022-05)
      Article
      Open Access
      Abstract Motivation The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top of common biomolecular simulation and bioinformatics tools. The possibility to access the library remotely and ...

    • BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations 

      Bayarri, Genís; Andrio, Pau; Hospital, Adam; Orozco, Modesto; Gelpi, Josep (Oxford University Press, 2022-07)
      Article
      Open Access
      We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building ...

    • 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 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 ...

    • 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 ...

    • 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 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 ...

    • 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 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, ...

    • Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows 

      Bayarri, Genís; Andrio, Pau; Gelpi, Josep; Hospital, Adam; Orozco, Modesto (Public Library of Science, 2024)
      Article
      Open Access
      Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming ...

    • 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 ...