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Found 219 results
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2025
The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters, Fort, Joana, Nicolàs-Aragó Adrià, Maggi Luca, Martinez-Molledo Maria, Kapiki Despoina, González-Novoa Paula, Gómez-Gejo Patricia, Zijlstra Niels, Bodoy Susanna, Pardon Els, et al. , PNAS Nexus, 01/2025, Volume 4, Issue 1, p.pgae584, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)
Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism, Genna, Vito, Portella Guillem, Sala Alba, Terrazas Montserrat, Serrano-Chacón Israel, González Javier, Villegas Núria, Mateo Lidia, Castellazzi Chiara, Labrador Mireia, et al. , Nucleic Acids Research, 03/2025, Volume 53, Issue 5, p.gkaf170, (2025)
Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism, Genna, Vito, Portella Guillem, Sala Alba, Terrazas Montserrat, Serrano-Chacón Israel, González Javier, Villegas Núria, Mateo Lidia, Castellazzi Chiara, Labrador Mireia, et al. , Nucleic Acids Research, 03/2025, Volume 53, Issue 5, p.gkaf170, (2025)
2024
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)
An integrated machine-learning model to predict nucleosome architecture, Sala, Alba, Labrador Mireia, Buitrago Diana, de Jorge Pau, Battistini Federica, Heath Isabelle Brun, and Orozco Modesto , Nucleic Acids Research, 09/2024, Volume 52, Issue 17, p.10132 - 10143, (2024)
Molecular stripping underpins derepression of a toxin–antitoxin system, Grabe, Grzegorz J., Giorgio Rachel T., Wieczór Miłosz, Gollan Bridget, Sargen Molly, Orozco Modesto, Hare Stephen A., and Helaine Sophie , Nat Struct Mol Biol, 2024/03/27, (2024)
RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)
RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)
RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)
SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)
Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells, Mir, Bartomeu, Serrano-Chacón Israel, Medina Pedro, Macaluso Veronica, Terrazas Montserrat, Gandioso Albert, Garavís Miguel, Orozco Modesto, Escaja Núria, and González Carlos , Nucleic Acids Res, 04/2024, Volume 52, Issue 6, p.3375 - 3389, (2024)
2023
Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway, González, Lorena, Díaz Lucía, Pous Joan, Baginski Blazej, Duran-Corbera Anna, Scarpa Margherita, Brun-Heath Isabelle, Igea Ana, Martin-Malpartida Pau, Ruiz Lidia, et al. , Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)
Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway, González, Lorena, Díaz Lucía, Pous Joan, Baginski Blazej, Duran-Corbera Anna, Scarpa Margherita, Brun-Heath Isabelle, Igea Ana, Martin-Malpartida Pau, Ruiz Lidia, et al. , Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)
Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides, Genna, Vito, Iglesias-Fernández Javier, Reyes-Fraile Laura, Villegas Núria, Guckian Kevin, Seth Punit, Wan Brad, Cabrero Cristina, Terrazas Montserrat, Brun-Heath Isabelle, et al. , Nucleic Acids Research, 06/2023, Volume 51, Issue 10, p.4713 - 4725, (2023)
Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides, Genna, Vito, Iglesias-Fernández Javier, Reyes-Fraile Laura, Villegas Núria, Guckian Kevin, Seth Punit, Wan Brad, Cabrero Cristina, Terrazas Montserrat, Brun-Heath Isabelle, et al. , Nucleic Acids Research, 06/2023, Volume 51, Issue 10, p.4713 - 4725, (2023)
Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair, Parisis, Nikolaos, Dans Pablo D., Jbara Muhammad, Singh Balveer, Schausi-Tiffoche Diane, Molina-Serrano Diego, Brun-Heath Isabelle, Hendrychová Denisa, Maity Suman Kumar, Buitrago Diana, et al. , Nature Communications, 08/2023, Volume 14, Issue 1, p.5104, (2023)
Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair, Parisis, Nikolaos, Dans Pablo D., Jbara Muhammad, Singh Balveer, Schausi-Tiffoche Diane, Molina-Serrano Diego, Brun-Heath Isabelle, Hendrychová Denisa, Maity Suman Kumar, Buitrago Diana, et al. , Nature Communications, 08/2023, Volume 14, Issue 1, p.5104, (2023)
pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs, Serrano-Chacón, Israel, Mir Bartomeu, Cupellini Lorenzo, Colizzi Francesco, Orozco Modesto, Escaja Núria, and González Carlos , Journal of the American Chemical Society, 02/2023, Volume 145, Issue 6, p.3696 - 3705, (2023)
Sequence-Dependent Properties of the RNA Duplex, Battistini, Federica, Sala Alba, Hospital Adam, and Orozco Modesto , Journal of Chemical Information and Modeling, 08/2023, Volume 63, Issue 16, p.5259 - 5271, (2023)
Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria, Naón, Déborah, Hernández-Alvarez María Isabel, Shinjo Satoko, Wieczor Milosz, Ivanova Saška, de Brito Olga Martins, Quintana Albert, Hidalgo Juan, Palacín Manuel, Aparicio Pilar, et al. , Science, 07/2023, Volume 380, Issue 6651, p.eadh9351, (2023)
Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria, Naón, Déborah, Hernández-Alvarez María Isabel, Shinjo Satoko, Wieczor Milosz, Ivanova Saška, de Brito Olga Martins, Quintana Albert, Hidalgo Juan, Palacín Manuel, Aparicio Pilar, et al. , Science, 07/2023, Volume 380, Issue 6651, p.eadh9351, (2023)
Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria, Naón, Déborah, Hernández-Alvarez María Isabel, Shinjo Satoko, Wieczor Milosz, Ivanova Saška, de Brito Olga Martins, Quintana Albert, Hidalgo Juan, Palacín Manuel, Aparicio Pilar, et al. , Science, 07/2023, Volume 380, Issue 6651, p.eadh9351, (2023)
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism, Tarrés-Solé, Aleix, Battistini Federica, Gerhold Joachim M., Piétrement Olivier, Martínez-García Belén, Ruiz-López Elena, Lyonnais Sébastien, Bernadó Pau, Roca Joaquim, Orozco Modesto, et al. , Nucleic Acids Research, 05/2023, p.gkad397, (2023)
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism, Tarrés-Solé, Aleix, Battistini Federica, Gerhold Joachim M., Piétrement Olivier, Martínez-García Belén, Ruiz-López Elena, Lyonnais Sébastien, Bernadó Pau, Roca Joaquim, Orozco Modesto, et al. , Nucleic Acids Research, 05/2023, p.gkad397, (2023)
Structural basis of a redox-dependent conformational switch that regulates the stress kinase p38α, Pous, Joan, Baginski Blazej, Martin-Malpartida Pau, González Lorena, Scarpa Margherita, Aragon Eric, Ruiz Lidia, Mees Rebeca A., Iglesias-Fernández Javier, Orozco Modesto, et al. , Nature Communications, 2023/12/01, Volume 14, Issue 1, p.7920, (2023)
2022
DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors, Barissi, Sandro, Sala Alba, Wieczór Miłosz, Battistini Federica, and Orozco Modesto , Nucleic Acids Res, 09/2022, Volume 50, Issue 16, (2022)
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, Jordá Luis, Orozco-Ruiz Sergi, Beltrán Daniel, Colizzi Francesco, Andrio Pau, Soliva Robert, Municoy Martí, et al. , Journal of Chemical Information and Modeling, 12/2022, Volume In press, (2022)
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, Jordá Luis, Orozco-Ruiz Sergi, Beltrán Daniel, Colizzi Francesco, Andrio Pau, Soliva Robert, Municoy Martí, et al. , Journal of Chemical Information and Modeling, 12/2022, Volume In press, (2022)
Making Canonical Workflow Building Blocks Interoperable across Workflow Languages, Soiland-Reyes, Stian, Bayarri Genis, Andrio Pau, Long Robin, Lowe Douglas, Niewielska Ania, Hospital Adam, and Groth Paul , Data Intelligence, 2022, p.1 - 16, (2022)
The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)
The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)
2020
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)
Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery, Zivanovic, Sanja, Bayarri Genis, Colizzi Francesco, Moreno David, Gelpí Josep Lluis, Soliva Robert, Hospital Adam, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community), Orengo, C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, et al. , F1000Research, 04/2020, Volume 9, (2020)
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community), Orengo, C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, et al. , F1000Research, 04/2020, Volume 9, (2020)

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