Browsing by Author "Hospital, Adam"

Now showing items 1-14 of 14

    • 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 ...

    • BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows 

      Andrio, Pau; Hospital, Adam; Conejero Bañón, Javier; Jordá, Luis; del Pino, Marc; Codo, Laia; Soiland Reyes, Stian; Goble, Carole; Lezzi, Daniele; Badia Sala, Rosa Maria; Orozco López, Modesto; Gelpi Buchaca, Josep Lluís (Nature, 2019-09-10)
      Article
      Open Access
      In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed ...

    • High-throughput prediction of the impact of genetic variability on drug sensitivity and resistance patterns for clinically relevant epidermal growth factor receptor mutations from atomistic simulations 

      Suriñach, Aristarc; Hospital, Adam; Westermaier, Yvonne; Jorda, Luis; Orozco Ruiz, Sergi; Andrio, Pau; Gelpi, Josep (American Chemical Society, 2022)
      Article
      Open Access
      Mutations in the kinase domain of the epidermal growth factor receptor (EGFR) can be drivers of cancer and also trigger drug resistance in patients receiving chemotherapy treatment based on kinase inhibitors. A priori ...

    • 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 ...

    • Making Canonical Workflow Building Blocks Interoperable across Workflow Languages 

      Soiland Reyes, Stian; Bayarri, Genís; Andrio, Pau; Long, Robin; Lowe, Douglas; Niewielska, Ania; Hospital, Adam; Groth, Paul (MIT Press, 2022-03)
      Article
      Open Access
      We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages ...

    • 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) ...

    • Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: a use case 

      Wieczór, Milosz; Genna, Vito; Aranda Moratalla, Juan; Badia Sala, Rosa Maria; Gelpi Buchaca, Josep Lluís; Gapsys, Vytautas; de Groot, Bert L.; Lindahl, Erik; Municoy Terol, Martí; Hospital, Adam; Orozco López, Modesto (John Wiley & sons, 2023-01)
      Article
      Open Access
      Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We ...

    • 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 ...