Biblio

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn, Holger, Vidal Enrique, Ferreira Humberto J., Vizoso Miguel, Sayols Sergi, Gomez Antonio, Moran Sebastian, Boque-Sastre Raquel, Guil Sonia, Martinez-Cardus Anna, et al. , Genome Biology, 01/2016, Volume 17, p.11, (2016)

Exploring the Complete Mutational Space of the LDL receptor LA5 Domain Using Molecular Dynamics: Linking SNPs with Disease Phenotypes in Familial Hypercholesterolemia, Angarica, Vladimir Espinosa, Orozco Modesto, and Sancho Javier , Human Molecular Genetics, (2016)

Long-timescale dynamics of the Drew-Dickerson dodecamer., Dans, Pablo D., Danilāne Linda, Ivani Ivan, Dršata Tomáš, Lankaš Filip, Hospital Adam, Walther Jurgen, Pujagut Ricard Illa, Battistini Federica, Gelpí Josep-Lluis, et al. , Nucleic Acids Res, 2016 May 19, Volume 44, p.4052-66, (2016)

Multiscale simulation of DNA, Dans, Pablo D., Walther Jurgen, Gómez Hansel, and Orozco Modesto , Current Opinions in Structural Biology - Theory and simulation • Macromolecular machines 2016, 02/2016, Volume 37, p.29 - 45, (2016)

Mutations in JMJD1C are involved in Rett syndrome and intellectual disability., Sáez, Mauricio A., Fernández-Rodríguez Juana, Moutinho Catia, Sanchez-Mut Jose V., Gomez Antonio, Vidal Enrique, Petazzi Paolo, Szczesna Karolina, Lopez-Serra Paula, Lucariello Mario, et al. , Genet Med, 2016 Apr, Volume 18, Issue 4, p.378-85, (2016)

Nucleosome architecture throughout the cell cycle, Deniz, Ozgen, Flores Oscar, Aldea Martí, Soler-López Montserrat, and Orozco Modesto , Scientific Reports, 01/2016, Volume 6, p.19729 -, (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)

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)

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)

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)

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)

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA, Darré, Leonardo, Ivani Ivan, Dans Pablo D., Gómez Hansel, Hospital Adam, and Orozco Modesto , Journal of the American Chemical Society, 12/2016, Volume 138, Issue 50, p.16355 - 16363, (2016)

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations, Kuzmanic, Antonija, Sutto Ludovico, Saladino Giorgio, Nebreda Angel R., Gervasio Francesco L., and Orozco Modesto , eLife, 04/2017, Volume 6, p.e22175, (2017)

Chapter 7 Molecular Modelling of Nucleic Acids, Gómez, Hansel, Walther Jurgen, Darré Leonardo, Ivani Ivan, Dans Pablo D., and Orozco Modesto , Computational Tools for Chemical Biology, p.165 - 197, (2017)

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry, Porrini, Massimiliano, Rosu Frédéric, Rabin Clémence, Darré Leonardo, Gómez Hansel, Orozco Modesto, and Gabelica Valérie , ACS Central Science, 05/2017, Volume 3, Issue 5, p.454 - 461, (2017)

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins, Emperador, Agustí, and Orozco Modesto , Journal of Chemical Theory and Computation, 03/2017, Volume 13, Issue 3, p.1454 - 1461, (2017)

A DNA methylation map of human cancer at single base-pair resolution, Vidal, E, Sayols S, Moran S, Guillaumet-Adkins A, Schroeder M P., Royo R, Orozco Modesto, Gut M, Gut I, Lopez-Bigas N, et al. , Oncogene, 06/2017, p.1-10, (2017)

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells, Gandioso, Albert, Massaguer Anna, Villegas Núria, Salvans Cándida, Sanchez Dani, Brun-Heath Isabelle, Marchan Vicente, Orozco Modesto, and Terrazas Montserrat , Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)

How accurate are accurate force-fields for B-DNA?, Dans, Pablo D., Ivani Ivan, Hospital Adam, Portella Guillem, González Carlos, and Orozco Modesto , Nucleic Acids Research, 01/2017, Volume 45, Issue 7, p.4217-4230, (2017)

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs, Kotev, Martin, Manuel-Manresa Pilar, Hernando Elsa, Soto-Cerrato Vanessa, Orozco Modesto, Quesada Roberto, Pérez-Tomás Ricardo, and Guallar Victor , Journal of Chemical Information and Modeling, 08/2017, (2017)

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop, Cunha, Eva S., Sfriso Pedro, Rojas Adriana L., Hospital Adam, Orozco Modesto, and Abrescia Nicola G. A. , Structure, 01/2017, Volume 25, p.53-65, (2017)

Methods to Trace Conformational Transitions, Sfriso, Pedro, and Orozco Modesto , Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, p.215 - 244, (2017)

The Multiple Roles of Waters in Protein Solvation, Hospital, Adam, Candotti Michela, Gelpí Josep-Lluis, and Orozco Modesto , The Journal of Physical Chemistry B, 01/2017, Issue Klaus Schulten Memorial Issue, (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)

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)

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)

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)

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)

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)

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance, Pluta, Radoslaw, D. Boer Roeland, Lorenzo-Díaz Fabián, Russi Silvia, Gómez Hansel, Fernández-López Cris, Pérez-Luque Rosa, Orozco Modesto, Espinosa Manuel, and Coll Miquel , Proc. Natl. Acad. Sci, USA, 08/2017, Volume 114, Issue 32, p.E6526 - E6535, (2017)

Allosterism and signal transfer in DNA, Balaceanu, Alexandra, Pérez Alberto, Dans Pablo D., and Orozco Modesto , Nucleic Acids Research, 2018/09/06, Volume 46, Issue 15, p.7554 - 7565, (2018)

Challenges and guidelines toward 4D nucleome data and model standards, Marti-Renom, Marc A., Almouzni Genevieve, Bickmore Wendy A., Bystricky Kerstin, Cavalli Giacomo, Fraser Peter, Gasser Susan M., Giorgetti Luca, Heard Edith, Nicodemi Mario, et al. , Nature Genetics, 10/2018, Volume 50, Issue 10, p.1352 - 1358, (2018)

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)

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)

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes, Garcia-Lopez, Amparo, Tessaro Francesca, Jonker Hendrik R. A., Wacker Anna, Richter Christian, Comte Arnaud, Berntenis Nikolaos, Schmucki Roland, Hatje Klas, Petermann Olivier, et al. , Nature Communication, 2018/05/23, Volume 9, Issue 1, p.2032, (2018)

The Yottaflop Frontier of Atomistic Molecular Dynamics Simulations, J Goñi, Ramon, and Orozco Modesto , Theoretical and Quantum Chemistry at the Dawn of the 21st Century, p.597-616, (2018)

Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease, Hernández-Alvarez, María Isabel, Sebastián David, Vives Sara, Ivanova Saška, Bartoccioni Paola, Kakimoto Pamela, Plana Natalia, Veiga Sónia R., Hernández Vanessa, Vasconcelos Nuno, et al. , Cell, 05/2019, Volume 177, Issue 4, p.881 - 895.e17, (2019)

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition, Battistini, Federica, Hospital Adam, Buitrago Diana, Gallego Diego, Dans Pablo D., Gelpí Josep Lluis, and Orozco Modesto , Journal of Molecular Biology, 07/2019, (2019)

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations, Kuzmanic, Antonija, Dans Pablo D., and Orozco Modesto , Chem, 03/2019, Volume 5, Issue 3, p.649 - 663, (2019)

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond, Balaceanu, Alexandra, Buitrago Diana, Walther Jurgen, Hospital Adam, Dans Pablo D., and Orozco Modesto , 01/2019, (2019)

A multifunctional toolkit for target-directed cancer therapy, Terrazas, Montserrat, Sanchez Dani, Battistini Federica, Villegas Núria, Brun-Heath Isabelle, and Orozco Modesto , Chemical Communications, 2019, Volume 55, Issue 6, p.802 - 805, (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)

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)

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)

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)

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids, Arangundy-Franklin, Sebastian, Taylor Alexander I., Porebski Benjamin T., Genna Vito, Peak-Chew Sew, Vaisman Alexandra, Woodgate Roger, Orozco Modesto, and Holliger Philipp , Nature Chemistry, 04/2019, (2019)

VeriNA3d: an R package for nucleic acids data mining, Gallego, Diego, Darré Leonardo, Dans Pablo D., and Orozco Modesto , Bioinformatics, 07/2019, (2019)