Biblio

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)

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort, Beltrán, Daniel, Hospital Adam, Gelpí Josep Lluis, and Orozco Modesto , Nucleic Acids Res, 04/2024, Volume 52, Issue D1, p.D393 - D403, (2024)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design, Genna, Vito, Reyes-Fraile Laura, Iglesias-Fernández Javier, and Orozco Modesto , Current Opinion in Structural Biology, 08/2024, Volume 87, p.102838, (2024)

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning, Buitrago, Diana, Codó Laia, Illa Ricard, de Jorge Pau, Battistini Federica, Flores Oscar, Bayarri Genis, Royo Romina, Del Pino Marc, Heath Simon, et al. , Nucleic Acids Research, 08/2019, (2019)

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope, Orellana, Laura, Thorne Amy H., Lema Rafael, Gustavsson Johan, Parisian Alison D., Hospital Adam, Cordeiro Tiago N., Bernadó Pau, Scott Andrew M., Brun-Heath Isabelle, et al. , Proceedings of the National Academy of Sciences, 04/2019, (2019)

On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates., Soteras, Ignacio, Lozano Oscar, Gómez-Esqué Arantxa, Escolano Carmen, Orozco Modesto, Amat Mercedes, Bosch Joan, and F Luque Javier , J Am Chem Soc, 2006 May 24, Volume 128, p.6581-8, (2006)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems., Emperador, Agustí, Sfriso Pedro, Villarreal Marcos Ariel, Gelpí Josep-Lluis, and Orozco Modesto , J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Partition of protein solvation into group contributions from molecular dynamics simulations., Morreale, Antonio, de la Cruz Xavier, Meyer Tim, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto , Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)

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)

PMUT: a web-based tool for the annotation of pathological mutations on proteins., Ferrer-Costa, Carles, Gelpí Josep-Lluis, Zamakola Leire, Párraga Iván, de la Cruz Xavier, and Orozco Modesto , Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update, López-Ferrando, Víctor, Gazzo Andrea, de la Cruz Xavier, Orozco Modesto, and Gelpí Josep-Lluis , Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update, López-Ferrando, Víctor, Gazzo Andrea, de la Cruz Xavier, Orozco Modesto, and Gelpí Josep-Lluis , Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH, Mir, Bartomeu, Serrano Israel, Buitrago Diana, Orozco Modesto, Escaja Núria, and González Carlos , Journal of the American Chemical Society, 11/2017, Volume 139, Issue 40, p.13985 - 13988, (2017)

Principles for designing proteins with cavities formed by curved β sheets, Marcos, Enrique, Basanta Benjamin, Chidyausiku Tamuka M., Tang Yuefeng, Oberdorfer Gustav, Liu Gaohua, Swapna G V. T., Guan Rongjin, Silva Daniel-Adriano, Dou Jiayi, et al. , Science (New York, N.Y.), 01/2017, Volume 355, Issue 6321, p.201 - 206, (2017)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution, Rubio-Cosials, Anna, Battistini Federica, Gansen Alexander, Cuppari Anna, Bernadó Pau, Orozco Modesto, Langowski Jörg, Tóth Katalin, and Solà Maria , Biophysical Journal, 05/2018, Volume 114, p.2386 - 2396, (2018)

Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)

Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)

Proton Dynamics in Protein Mass Spectrometry, Li, Jinyu, Lyu Wenping, Rossetti Giulia, Konijnenberg Albert, Natalello Antonino, Ippoliti Emiliano, Orozco Modesto, Sobott Frank, Grandori Rita, and Carloni Paolo , The Journal of Physical Chemistry Letters, 03/2017, Volume 8, Issue 6, p.1105 - 1112, (2017)

The pseudotorsional space of RNA, Grille, Leandro, Gallego Diego, Darré Leonardo, da Rosa Gabriela, Battistini Federica, Orozco Modesto, and Dans Pablo D. , RNA, 12/2023, Volume 29, Issue 12, p.1896 - 1909, (2023)

The pseudotorsional space of RNA, Grille, Leandro, Gallego Diego, Darré Leonardo, da Rosa Gabriela, Battistini Federica, Orozco Modesto, and Dans Pablo D. , RNA, 12/2023, Volume 29, Issue 12, p.1896 - 1909, (2023)

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data, Shkurti, Ardita, Goni Ramon, Andrio Pau, Breitmoser Elena, Bethune Iain, Orozco Modesto, and Laughton Charles A. , SoftwareX, 12/2016, Volume 5, p.44 - 50, (2016)

QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism, Gómez, Hansel, Mendoza Fernanda, Lluch José M., and Masgrau Laura , Advances in Protein Chemistry and Structural Biology, p.-, (2015)

QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism, Gómez, Hansel, Mendoza Fernanda, Lluch José M., and Masgrau Laura , Advances in Protein Chemistry and Structural Biology, Volume 100, p.-, (2015)

Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state., Gómez, Hansel, Polyak Iakov, Thiel Walter, Lluch José M., and Masgrau Laura , J Am Chem Soc, 2012 Mar 14, Volume 134, p.4743-52, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

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)

Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis., Lama, Amrita, Pawaria Sudesh, Bidon-Chanal Axel, Anand Arvind, Gelpí Josep-Lluis, Arya Swati, Martí Marcelo, Estrin Darío A., F Luque Javier, and Dikshit Kanak L. , J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)

SAR and 3D-QSAR studies on thiadiazolidinone derivatives: exploration of structural requirements for glycogen synthase kinase 3 inhibitors., Martínez, Ana, Alonso Mercedes, Castro Ana, Dorronsoro Isabel, Gelpí Josep-Lluis, F Luque Javier, Pérez Concepción, and Moreno Francisco J. , J Med Chem, 2005 Nov 17, Volume 48, p.7103-12, (2005)