Search Results - "Gelpí, Josep Lluís"

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations by Bayarri, Genís, Andrio, Pau, Hospital, Adam, Orozco, Modesto, Gelpí, Josep Lluís

“…Abstract We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal…”
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The Multiple Roles of Waters in Protein Solvation by Hospital, Adam, Candotti, Michela, Gelpí, Josep Lluís, Orozco, Modesto

“…Extensive molecular dynamics (MD) simulations have been used to characterize the multiple roles of water in solvating different types of proteins under…”
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Genome-wide pathway analysis identifies VEGF pathway association with oral ulceration in systemic lupus erythematosus by Aterido, Adrià, Julià, Antonio, Carreira, Patricia, Blanco, Ricardo, López-Longo, José Javier, Venegas, José Javier Pérez, Olivé, Àlex, Andreu, José Luís, Aguirre-Zamorano, Maria Ángeles, Vela, Paloma, Nolla, Joan M, Marenco-de la Fuente, José Luís, Zea, Antonio, Pego, José María, Freire, Mercedes, Díez, Elvira, López-Lasanta, María, López-Corbeto, Mireia, Palau, Núria, Tortosa, Raül, Gelpí, Josep Lluís, Absher, Devin, Myers, Richard M, Fernández-Nebro, Antonio, Marsal, Sara

“…Systemic lupus erythematosus (SLE) is a genetically complex rheumatic disease characterized by heterogeneous clinical manifestations of unknown etiology…”
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A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort by Beltrán, Daniel, Hospital, Adam, Gelpí, Josep Lluís, Orozco, Modesto

“…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…”
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Evidence for transcript networks composed of chimeric RNAs in human cells by Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M, Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline, Ribeca, Paolo, Martin, David, Murray, Ryan R, Yang, Xinping, Ghamsari, Lila, Lin, Chenwei, Bell, Ian, Dumais, Erica, Drenkow, Jorg, Tress, Michael L, Gelpí, Josep Lluís, Orozco, Modesto, Valencia, Alfonso, van Berkum, Nynke L, Lajoie, Bryan R, Vidal, Marc, Stamatoyannopoulos, John, Batut, Philippe, Dobin, Alex, Harrow, Jennifer, Hubbard, Tim, Dekker, Job, Frankish, Adam, Salehi-Ashtiani, Kourosh, Reymond, Alexandre, Antonarakis, Stylianos E, Guigó, Roderic, Gingeras, Thomas R

“…The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical…”
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FAIRsoft-a practical implementation of FAIR principles for research software by Martín Del Pico, Eva, Gelpí, Josep Lluís, Capella-Gutierrez, Salvador

“…Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce…”
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Surviving the deluge of biosimulation data by Hospital, Adam, Battistini, Federica, Soliva, Robert, Gelpí, Josep Lluis, Orozco, Modesto

“…New hardware, massively parallel and graphical processing unit‐based computers in particular, has boosted molecular simulations to levels that would be…”
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PMUT: a web-based tool for the annotation of pathological mutations on proteins by Ferrer-Costa, Carles, Gelpí, Josep Lluis, Zamakola, Leire, Parraga, Ivan, de la Cruz, Xavier, Orozco, Modesto

“…PMUT allows the fast and accurate prediction (~80% success rate in humans) of the pathological character of single point amino acidic mutations based on the…”
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PACSAB: Coarse-Grained Force Field for the Study of Protein–Protein Interactions and Conformational Sampling in Multiprotein Systems by Emperador, Agustí, Sfriso, Pedro, Villarreal, Marcos Ariel, Gelpí, Josep Lluis, Orozco, Modesto

“…Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule…”
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Metadata to Describe Genomic Information by Delgado, Jaime, Naro, Daniel, Llorente, Silvia, Gelpí, Josep Lluís, Royo, Romina

“…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…”
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Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale: e1003393 by Candotti, Michela, Pérez, Alberto, Ferrer-Costa, Carles, Rueda, Manuel, Meyer, Tim, Gelpí, Josep Lluís, Orozco, Modesto

“…After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein…”
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Parmbsc1: a refined force field for DNA simulations by Ivani, Ivan, Dans, Pablo D, Noy, Agnes, Pérez, Alberto, Faustino, Ignacio, Hospital, Adam, Walther, Jürgen, Andrio, Pau, Goñi, Ramon, Balaceanu, Alexandra, Portella, Guillem, Battistini, Federica, Gelpí, Josep Lluis, González, Carlos, Vendruscolo, Michele, Laughton, Charles A, Harris, Sarah A, Case, David A, Orozco, Modesto

“…Parmbsc1, a new force field for DNA simulations, was broadly tested on nearly 100 DNA systems and overcame simulation artifacts that affected previous force…”
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Long-timescale dynamics of the Drew-Dickerson dodecamer by Dans, Pablo D, Danilāne, Linda, Ivani, Ivan, Dršata, Tomáš, Lankaš, Filip, Hospital, Adam, Walther, Jürgen, Pujagut, Ricard Illa, Battistini, Federica, Gelpí, Josep Lluis, Lavery, Richard, Orozco, Modesto

“…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…”
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Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug Discovery by Zivanovic, Sanja, Bayarri, Genís, Colizzi, Francesco, Moreno, David, Gelpí, Josep Lluís, Soliva, Robert, Hospital, Adam, Orozco, Modesto

“…Modern high-throughput structure-based drug discovery algorithms consider ligand flexibility, but typically with low accuracy, which results in a loss of…”
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MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations by HOSPITAL, Adam, ANDRIO, Pau, FENOLLOSA, Carles, CICIN-SAIN, Damjan, OROZCO, Modesto, LLUIS GELPI, Josep

“…MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides…”
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Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows by Bayarri, Genís, Andrio, Pau, Gelpí, Josep Lluís, Hospital, Adam, Orozco, Modesto

“…Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and…”
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MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories by Meyer, Tim, D'Abramo, Marco, Hospital, Adam, Rueda, Manuel, Ferrer-Costa, Carles, Pérez, Alberto, Carrillo, Oliver, Camps, Jordi, Fenollosa, Carles, Repchevsky, Dmitry, Gelpí, Josep Lluis, Orozco, Modesto

“…More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means…”
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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 by Suriñach, Aristarc, Hospital, Adam, Westermaier, Yvonne, Jordà, Luis, Orozco-Ruiz, Sergi, Beltrán, Daniel, Colizzi, Francesco, Andrio, Pau, Soliva, Robert, Municoy, Martí, Gelpí, Josep Lluís, Orozco, Modesto

“…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…”
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FlexServ: an integrated tool for the analysis of protein flexibility by Camps, Jordi, Carrillo, Oliver, Emperador, Agustí, Orellana, Laura, Hospital, Adam, Rueda, Manuel, Cicin-Sain, Damjan, D'Abramo, Marco, Gelpí, Josep Lluís, Orozco, Modesto

“…FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of…”
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consensus view of protein dynamics by Rueda, Manuel, Ferrer-Costa, Carles, Meyer, Tim, Pérez, Alberto, Camps, Jordi, Hospital, Adam, Gelpí, Josep Lluis, Orozco, Modesto

“…The dynamics of proteins in aqueous solution has been investigated through a massive approach based on "state of the art" molecular dynamics simulations…”
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