Search Results - "Gelpi, Josep Lluis"

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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Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations by Sfriso, Pedro, Emperador, Agusti, Orellana, Laura, Hospital, Adam, Gelpí, Josep Lluis, Orozco, Modesto

“…We present a new method for estimating pathways for conformational transitions in macromolecules from the use of discrete molecular dynamics and biasing…”
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Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice by Ramírez-Bajo, Maria José, de Atauri, Pedro, Ortega, Fernando, Westerhoff, Hans V, Gelpí, Josep Lluis, Centelles, Josep J, Cascante, Marta

“…The effects of pre-incubation with mercury (Hg(2+)) and cadmium (Cd(2+)) on the activities of individual glycolytic enzymes, on the flux and on internal…”
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Exploring early stages of the chemical unfolding of proteins at the proteome scale 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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Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes by JULIA, Antonio, TORTOSA, Raül, RODRIGUEZ, Jesus, GRATACOS, Jordi, DAUDEN, Esteban, SANCHEZ-CARAZO, José Luís, LOPEZ-ESTEBARANZ, José Luís, MORENO-RAMIREZ, David, QUEIRO, Rubén, MONTILLA, Carlos, TORRE-ALONSO, Juan Carlos, PEREZ-VENEGAS, José Javier, HERNANZ, José Manuel, VANACLOCHA, Francisco, HERRERA, Enrique, MUNOZ-FERNANDEZ, Santiago, GONZALEZ, Carlos, ROIG, Daniel, ERRA, Alba, ACOSTA, Isabel, FERNANDEZ-NEBRO, Antonio, ZARCO, Pedro, ALONSO, Arnald, CANETE, Juan D, LOPEZ-LASANTA, Maria, GARCIA-MONTERO, Andrés, LLUIS GELPI, Josep, ABSHER, Devin, MARSAL, Sara, FONSECA, Eduardo, FERRANDIZ, Carlos, UNAMUNO, Pablo, PUIG, Lluís, FERNANDEZ-SUEIRO, José Luís, SANMARTI, Raimon

“…Recent genome-wide association studies (GWASs) have identified >20 new loci associated with the susceptibility to psoriasis vulgaris (PsV) risk. We…”
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Inntags: small self-structured epitopes for innocuous protein tagging by Georgieva, Maya V, Yahya, Galal, Codó, Laia, Ortiz, Raúl, Teixidó, Laura, Claros, José, Jara, Ricardo, Jara, Mònica, Iborra, Antoni, Gelpí, Josep Lluís, Gallego, Carme, Orozco, Modesto, Aldea, Martí

“…A set of small, innocuous protein tags, named inntags, show advantages over commonly used epitope tags in a variety of biological applications. Protein tagging…”
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A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300 by Julià, Antonio, Domènech, Eugeni, Ricart, Elena, Tortosa, Raül, García-Sánchez, Valle, Gisbert, Javier P, Nos Mateu, Pilar, Gutiérrez, Ana, Gomollón, Fernando, Mendoza, Juan Luís, Garcia-Planella, Esther, Barreiro-de Acosta, Manuel, Muñoz, Fernando, Vera, Maribel, Saro, Cristina, Esteve, Maria, Andreu, Montserrat, Alonso, Arnald, López-Lasanta, María, Codó, Laia, Gelpí, Josep Lluís, García-Montero, Andres C, Bertranpetit, Jaume, Absher, Devin, Panés, Julián, Marsal, Sara

“…Genome-wide association studies (GWAS) have identified multiple risk loci for Crohn's disease (CD). However, the cumulative risk exerted by these loci is low,…”
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Assessment of Human SARS CoV-2-Specific T-Cell Responses Elicited In Vitro by New Computationally Designed mRNA Immunogens (COVARNA) by Esteban, Ignasi, Pastor-Quiñones, Carmen, Usero, Lorena, Aurrecoechea, Elena, Franceschini, Lorenzo, Esprit, Arthur, Gelpí, Josep Lluís, Martínez-Jiménez, Francisco, López-Bigas, Núria, Breckpot, Karine, Thielemans, Kris, Leal, Lorna, Gómez, Carmen Elena, Sisteré-Oró, Marta, Meyerhans, Andreas, Esteban, Mariano, Alonso, María José, García, Felipe, Plana, Montserrat

“…The COVID-19 pandemic has brought significant changes and advances in the field of vaccination, including the implementation and widespread use of encapsidated…”
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BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools by Bayarri, Genís, Andrio, Pau, Hospital, Adam, Orozco, Modesto, Gelpí, Josep Lluís

“…Abstract Motivation The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top of common biomolecular simulation and…”
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Dissection of the Recognition Properties of p38 MAP Kinase. Determination of the Binding Mode of a New Pyridinyl−Heterocycle Inhibitor Family by Soliva, Robert, Gelpí, Josep Lluis, Almansa, Carmen, Virgili, Marina, Orozco, Modesto

“…The main recognition characteristics of the ATP binding site of p38 mitogen activated protein kinase alpha (p38α MAPK) have been explored by a combination of…”
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How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition by Battistini, Federica, Hospital, Adam, Buitrago, Diana, Gallego, Diego, Dans, Pablo D., Gelpí, Josep Lluis, Orozco, Modesto

“…The rules governing sequence-specific DNA–protein recognition are under a long-standing debate regarding the prevalence of base versus shape readout mechanisms…”
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Cohort Profile: The Cardiovascular Research Data Catalogue by Reinikainen, Jaakko, Palosaari, Tarja, Canosa-Valls, Alejandro J, Schmidt, Carsten O, Wissa, Rita, Chadalavada, Sucharitha, Codó, Laia, Gelpí, Josep Lluís, Joseph, Bijoy, van der Lugt, Aad, Pacella, Elsa, Petersen, Steffen E, Pujadas, Esmeralda Ruiz, Szabo, Liliana, Zeller, Tanja, Niiranen, Teemu, Lekadir, Karim, Kuulasmaa, Kari

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