Browsing by Author "Hospital, Adam"
Now showing items 1-14 of 14
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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 AccessAbstract 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 AccessMolecular 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 AccessMolecular 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 AccessAbstract 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 AccessWe 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)
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Open AccessIn 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 AccessMutations 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 AccessWe 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)
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Open AccessWe 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 AccessWe 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)
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Open AccessWe 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)
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Open AccessExascale 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 AccessExtensive 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 AccessInteractive 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 ...