Biblio

Oncogenic mutations of the EGF-Receptor ectodomain reveal an unexpected mechanism for ligand-independent activation, Orellana, Laura, Hospital Adam, and Orozco Modesto , bioRxiv, 09/2014, (2014)

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)

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)

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)

On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling"., Klamt, Andreas, Mennucci Benedetta, Tomasi Jacopo, Barone Vincenzo, Curutchet Carles, Orozco Modesto, and F Luque Javier , Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)

Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies., Soteras, Ignacio, Forti Flavio, Orozco Modesto, and F Luque Javier , J Phys Chem B, 2009 Jul 9, Volume 113, p.9330-4, (2009)

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies., Soteras, Ignacio, Orozco Modesto, and F Luque Javier , J Comput Aided Mol Des, 2010 Apr, Volume 24, p.281-91, (2010)

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)

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., Deniz, Ozgen, Flores Oscar, Battistini Federica, Pérez Alberto, Soler-López Montserrat, and Orozco Modesto , BMC Genomics, 2011, Volume 12, p.489, (2011)

Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor, Fernández-Zapata, Jesús, Pérez-Castaño Ricardo, Aranda Juan, Colizzi Francesco, Polanco María Carmen, Orozco Modesto, Padmanabhan S., and Elías-Arnanz Montserrat , Journal of Biological Chemistry, 11/2018, Volume 293, Issue 46, p.17888 - 17905, (2018)

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)

Polarization effects in molecular interactions, F Luque, Javier, Dehez François, Chipot Christophe, and Orozco Modesto , WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (2011)

Predicting the limit of intramolecular H-Bonding with classical molecular dynamics, Colizzi, Francesco, Hospital Adam, Zivanovic Sanja, and Orozco Modesto , Angewandte Chemie International Edition, 01/2019, (2019)

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations, Orellana, Laura, Yoluk Ozge, Carrillo Oliver, Orozco Modesto, and Lindahl Erik , Nat Commun, 2016/08/31, Volume 7, (2016)

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations, Orellana, Laura, Yoluk Ozge, Carrillo Oliver, Orozco Modesto, and Lindahl Erik , Nat Commun, 2016/08/31, Volume 7, (2016)

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)

Probing allosteric regulations with coevolution-driven molecular simulations, Colizzi, Francesco, and Orozco Modesto , Science advances, 10/2021, Volume 7, Issue 37, p.eabj0786 - eabj0786, (2021)

A procedure for identifying homologous alternative splicing events., Talavera, David, Hospital Adam, Orozco Modesto, and de la Cruz Xavier , BMC Bioinformatics, 2007, Volume 8, p.260, (2007)

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)

Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials., Emperador, Agustí, Meyer Tim, and Orozco Modesto , Proteins, 2010 Jan, Volume 78, p.83-94, (2010)

The protein folding transition-state ensemble from a Go-like model., Naganathan, Athi N., and Orozco Modesto , Phys Chem Chem Phys, 2011 Sep 7, Volume 13, p.15166-74, (2011)

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)

Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study, Paulikat, Mirko, Aranda Juan, Ippoliti Emiliano, Orozco Modesto, and Carloni Paolo , The Journal of Physical Chemistry Letters, 12/2022, Volume 13, Issue 51, p.12004 - 12010, (2022)

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes., Conde, Lucía, Vaquerizas Juan M., Ferrer-Costa Carles, de la Cruz Xavier, Orozco Modesto, and Dopazo Joaquin , Nucleic Acids Res, 2005 Jul 1, Volume 33, p.W501-5, (2005)

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)

Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer, Jaeger, Samira, Igea Ana, Arroyo Rodrigo, Alcalde Victor, Canovas Begoña, Orozco Modesto, Nebreda Angel R., and Aloy Patrick , Cancer Research, 01/2017, Volume 77, Issue 2, p.459, (2017)

Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression, Terrazas, Montserrat, Ivani Ivan, Villegas Núria, Paris Clément, Salvans Cándida, Brun-Heath Isabelle, and Orozco Modesto , Nucleic Acids Research, 11/2016, Volume 44, p.4354-4367, (2016)

Real-time atomistic description of DNA unfolding., Pérez, Alberto, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)

Recent advances in the study of nucleic acid flexibility by molecular dynamics., Orozco, Modesto, Noy Agnes, and Pérez Alberto , Curr Opin Struct Biol, 2008 Apr, Volume 18, p.185-93, (2008)

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers., Pérez, Alberto, Marchán Ivan, Svozil Daniel, Sponer Jiri, Cheatham Thomas E., Laughton Charles A., and Orozco Modesto , Biophys J, 2007 Jun 1, Volume 92, p.3817-29, (2007)

The relative flexibility of B-DNA and A-RNA duplexes: database analysis., Pérez, Alberto, Noy Agnes, Lankaš Filip, F Luque Javier, and Orozco Modesto , Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)

Relative flexibility of DNA and RNA: a molecular dynamics study., Noy, Agnes, Pérez Alberto, Lankaš Filip, F Luque Javier, and Orozco Modesto , J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)

Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH, Mazouzi, Abdelghani, Battistini Federica, Moser Sarah C., da Silva Joana Ferreira, Wiedner Marc, Owusu Michel, Lardeau Charles-Hugues, Ringler Anna, Weil Beatrix, Neesen Jürgen, et al. , Molecular Cell, 11/2017, Volume 68, Issue 4, p.797 - 807, (2017)

Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH, Mazouzi, Abdelghani, Battistini Federica, Moser Sarah C., da Silva Joana Ferreira, Wiedner Marc, Owusu Michel, Lardeau Charles-Hugues, Ringler Anna, Weil Beatrix, Neesen Jürgen, et al. , Molecular Cell, 11/2017, Volume 68, Issue 4, p.797 - 807, (2017)

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins, Sfriso, Pedro, Duran-Frigola Miquel, Mosca Roberto, Emperador Agustí, Aloy Patrick, and Orozco Modesto , Structure, Volume 24, p.116 - 126, (2016)

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA, Balaceanu, Alexandra, Pasi Marco, Dans Pablo D., Hospital Adam, Lavery Richard, and Orozco Modesto , The Journal of Physical Chemistry Letters, 01/01/2017, Volume 8, p.21 - 28, (2017)

Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking., Pons, Carles, Talavera David, de la Cruz Xavier, Orozco Modesto, and Fernandez-Recio Juan , J Chem Inf Model, 2011 Feb 28, Volume 51, p.370-7, (2011)

SEABED: Small molEcule activity scanner weB servicE baseD., Fenollosa, Carlos, Otón Marcel, Andrio Pau, Cortés Jorge, Orozco Modesto, and J Goñi Ramon , Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)

SEABED: Small molEcule activity scanner weB servicE baseD., Fenollosa, Carlos, Otón Marcel, Andrio Pau, Cortés Jorge, Orozco Modesto, and J Goñi Ramon , Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)

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)

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?, da Rosa, Gabriela, Grille Leandro, Calzada Victoria, Ahmad Katya, Arcon Juan Pablo, Battistini Federica, Bayarri Genis, Bishop Thomas, Carloni Paolo, III Thomas Cheatham, et al. , Biophysical Reviews, 11/2021, (2021)

Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties, Habibian, Maryam, Martínez-Montero Saúl, Portella Guillem, Chua Zhijie, D. Bohle Scott, Orozco Modesto, and Damha Masad J. , Organic Letters, 11/2015, Volume 17, Issue 21, p.5416 - 5419, (2015)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)