Search Results - "Orozco López, Modesto"

How accurate are accurate force-fields for B-DNA? by Dans, Pablo D, Ivani, Ivan, Hospital, Adam, Portella, Guillem, González, Carlos, Orozco, Modesto

“…Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that…”
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The Differential Response of Proteins to Macromolecular Crowding by Candotti, Michela, Orozco, Modesto

“…The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense…”
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Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations by Orellana, Laura, Yoluk, Ozge, Carrillo, Oliver, Orozco, Modesto, Lindahl, Erik

“…Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along…”
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Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins by Emperador, Agustí, Orozco, Modesto

“…We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the…”
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Allosterism and signal transfer in DNA by Balaceanu, Alexandra, Pérez, Alberto, Dans, Pablo D, Orozco López, Modesto

“…We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex…”
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Allosterism and signal transfer in DNA by Balaceanu, Alexandra, Pérez, Alberto, Dans, Pablo D, Orozco, Modesto

“…Abstract We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex…”
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Prevalent Sequences in the Human Genome Can Form Mini i‑Motif Structures at Physiological pH by Mir, Bartomeu, Serrano, Israel, Buitrago, Diana, Orozco, Modesto, Escaja, Núria, González, Carlos

“…We report here the solution structure of several repetitive DNA sequences containing d­(TCGT­TCCGT) and related repeats. At physiological pH, these sequences…”
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Challenges of docking in large, flexible and promiscuous binding sites by Kotev, Martin, Soliva, Robert, Orozco López, Modesto

“…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…”
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Challenges of docking in large, flexible and promiscuous binding sites by Kotev, Martin, Soliva, Robert, Orozco López, Modesto

“…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…”
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Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond by Balaceanu, Alexandra, Buitrago, Diana, Walther, Jürgen, Hospital, Adam, Dans, Pablo D, Orozco, Modesto

“…Abstract We used extensive molecular dynamics simulations to study the structural and dynamic properties of the central d(TpA) step in the highly polymorphic…”
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Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins by Sfriso, Pedro, Duran-Frigola, Miquel, Mosca, Roberto, Emperador, Agustí, Aloy, Patrick, Orozco, Modesto

“…We present here a new approach for the systematic identification of functionally relevant conformations in proteins. Our fully automated pipeline, based on…”
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Multiscale simulation of DNA by Dans, Pablo D, Walther, Jürgen, Gómez, Hansel, Orozco López, Modesto

“…DNA is not only among the most important molecules in life, but a meeting point for biology, physics and chemistry, being studied by numerous techniques…”
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Prevalent sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH by Mir Morro, Bartomeu, Serrano, Israel, Buitrago, Diana, Orozco López, Modesto, Escaja Sánchez, Nuria, González, Carlos

“…We report here the solution structure of several repetitive DNA sequences containing d(TCGTTCCGT) and related repeats. At physiological pH, these sequences…”
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Prevalent sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH by Mir Morro, Bartomeu, Serrano, Israel, Buitrago, Diana, Orozco López, Modesto, Escaja Sánchez, Nuria, González, Carlos

“…We report here the solution structure of several repetitive DNA sequences containing d(TCGTTCCGT) and related repeats. At physiological pH, these sequences…”
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Prevalent sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH by Mir Morro, Bartomeu, Serrano, Israel, Buitrago, Diana, Orozco López, Modesto, Escaja Sánchez, Nuria, González, Carlos

“…We report here the solution structure of several repetitive DNA sequences containing d(TCGTTCCGT) and related repeats. At physiological pH, these sequences…”
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PMut. A web-based tool for the annotation of pathological variants on proteins, 2017 update by López Ferrando, Víctor, Gazzo, Andrea, de la Cruz, Xavier, Orozco López, Modesto, Gelpí Buchaca, Josep Lluís

“…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…”
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PMut. A web-based tool for the annotation of pathological variants on proteins, 2017 update by López Ferrando, Víctor, Gazzo, Andrea, de la Cruz, Xavier, Orozco López, Modesto, Gelpí Buchaca, Josep Lluís

“…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…”
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Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes by Garcia-Lopez, Amparo, Tessaro, Francesca, Jonker, Hendrik R. A., Wacker, Anna, Richter, Christian, Comte, Arnaud, Berntenis, Nikolaos, Schmucki, Roland, Hatje, Klas, Petermann, Olivier, Chiriano, Gianpaolo, Perozzo, Remo, Sciarra, Daniel, Konieczny, Piotr, Faustino, Ignacio, Fournet, Guy, Orozco, Modesto, Artero, Ruben, Metzger, Friedrich, Ebeling, Martin, Goekjian, Peter, Joseph, Benoît, Schwalbe, Harald, Scapozza, Leonardo

“…Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to…”
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Understanding the Connetion between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations by Portella, Guillem, Battistini, Federica, Orozco López, Modesto

“…Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of…”
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Understanding the Connetion between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations by Portella, Guillem, Battistini, Federica, Orozco López, Modesto

“…Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of…”
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