Biblio

De novo design of a non-local β-sheet protein with high stability and accuracy, Marcos, Enrique, Chidyausiku Tamuka M., McShan Andrew C., Evangelidis Thomas, Nerli Santrupti, Carter Lauren, Nivón Lucas G., Davis Audrey, Oberdorfer Gustav, Tripsianes Konstantinos, et al. , Nature structural & molecular biology, 11/2018, Volume 25, Issue 11, p.1028 - 1034, (2018)

Data mining of molecular dynamics trajectories of nucleic acids., Noy, Agnes, Meyer Tim, Rueda Manuel, Ferrer Carles, Valencia Antonion, Pérez Alberto, de la Cruz Xavier, López-Bes J M., Pouplana R, Fernandez-Recio J, et al. , J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)

DASiR: Distributed Annotation System in R, Flores, Oscar, and Mantsoki Anna , (2013)

Cystinuria-specific rBAT(R365W) mutation reveals two translocation pathways in the amino acid transporter rBAT-b0,+AT., Pineda, Marta, Wagner Carsten A., Bröer Angelika, Stehberger Paul A., Kaltenbach Simone, Gelpí Josep-Lluis, Del Río Rafael Martín, Zorzano Antonio, Palacín Manuel, Lang Florian, et al. , Biochem J, 2004 Feb 1, Volume 377, p.665-74, (2004)

Correlated motions in DNA: beyond base-pair step models of DNA flexibility, López-Güell, Kim, Battistini Federica, and Orozco Modesto , Nucleic Acids Research, 06/2023, Volume 51, Issue 6, p.2633 - 2640, (2023)

Correlated motions are a fundamental property of B-sheets, R. Fenwick, Bryn, Orellana Laura, Esteban-Martí-n Santi, Orozco Modesto, and Salvatella Xavier , Nat Commun, 10/2014, Volume 5, (2014)

Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study, Harris, Sarah A., Gavathiotis Evripidis, Searle Mark S., Orozco Modesto, and Laughton Charles A. , Journal of the American Chemical Society, 2001/12/01, Volume 123, Issue 50, p.12658 - 12663, (2001)

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)

Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase., Trejo, F, Gelpí Josep-Lluis, Ferrer A, Boronat A, Busquets M, and Cortés A , Protein Eng, 2001 Nov, Volume 14, p.911-7, (2001)

Continuum and discrete calculation of fractional contributions to solvation free energy., Morreale, Antonio, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto , J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field, Jamroz, Michal, Orozco Modesto, Kolinski Andrzej, and Kmiecik Sebastian , Journal of Chemical Theory and Computation, 2013/01/08, Volume 9, Issue 1, p.119 - 125, (2012)

A consensus view of protein dynamics., Rueda, Manuel, Ferrer-Costa Carles, Meyer Tim, Pérez Alberto, Camps Jordi, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)

Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions., Signorelli, Santiago, Dans Pablo D., E Coitiño Laura, Borsani Omar, and Monza Jorge , PLoS One, 2015, Volume 10, p.e0115349, (2015)

Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer., Saneyoshi, Hisao, Mazzini Stefania, Aviñó Anna, Portella Guillem, González Carlos, Orozco Modesto, Marquez Victor E., and Eritja Ramon , Nucleic Acids Res, 2009 Sep, Volume 37, p.5589-601, (2009)

The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator., Naganathan, Athi Narayanan, and Orozco Modesto , The Journal of Physical Chemistry B, 2013/00/15, (2013)

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale., Islam, Barira, Sgobba Miriam, Laughton Charlie, Orozco Modesto, Sponer Jiri, Neidle Stephen, and Haider Shozeb , Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)

A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2., Gómez, Hansel, Rojas Raúl, Patel Divya, Tabak Lawrence A., Lluch José M., and Masgrau Laura , Org Biomol Chem, 2014 May 7, Volume 12, p.2645-55, (2014)

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads., Moncunill, Valentí, González Santi, Beà Sílvia, Andrieux Lise O., Salaverria Itziar, Royo Cristina, Martinez Laura, Puiggròs Montserrat, Segura-Wang Maia, Stütz Adrian M., et al. , Nat Biotechnol, 2014 Nov, Volume 32, p.1106-12, (2014)

Comparison of molecular dynamics and superfamily spaces of protein domain deformation., Velázquez-Muriel, Javier A., Rueda Manuel, Cuesta Isabel, Pascual-Montano Alberto, Orozco Modesto, and Carazo José-María , BMC Struct Biol, 2009, Volume 9, p.6, (2009)

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)

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 commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA, Battistini, Federica , Biophysical Reviews, 04/2024, (2024)

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer, Dziubańska-Kusibab, Paulina J., Berger Hilmar, Battistini Federica, Bouwman Britta A. M., Iftekhar Amina, Katainen Riku, Cajuso Tatiana, Crosetto Nicola, Orozco Modesto, Aaltonen Lauri A., et al. , Nature Medicine, 07/2020, Volume 26, Issue 7, p.1063 - 1069, (2020)

COCO: a simple tool to enrich the representation of conformational variability in NMR structures., Laughton, Charles A., Orozco Modesto, and Vranken Wim , Proteins, 2009 Apr, Volume 75, p.206-16, (2009)

Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings., Orozco, Modesto, Orellana Laura, Hospital Adam, Naganathan Athi N., Emperador Agustí, Carrillo Oliver, and Gelpí J L. , Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)

A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics, Dans, Pablo Daniel, Zeida Ari, Machado Matías R., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 5, p.1711–1725, (2010)

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins., Gelpí, Josep-Lluis, Kalko S G., Barril X, Cirera J, de La Cruz X, Luque F J., and Orozco Modesto , Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study, Collepardo-Guevara, Rosana, Portella Guillem, Vendruscolo Michele, Frenkel Daan, Schlick Tamar, and Orozco Modesto , Journal of the American Chemical Society, 2015/08/19, Volume 137, Issue 32, p.10205 - 10215, (2015)

Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms., Barbany, Montserrat, Morata Jordi, Meyer Tim, Lois Sergi, Orozco Modesto, and de la Cruz Xavier , Proteins, 2012 Aug, Volume 80, p.2235-49, (2012)

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 disease-associated single amino acid polymorphisms in terms of sequence and structure properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2002 Jan 25, Volume 315, p.771-86, (2002)

Characterization of compensated mutations in terms of structural and physico-chemical properties., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)

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)

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)

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)

The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors., Gracia, Eduard, Farré Daniel, Cortés Antoni, Ferrer-Costa Carles, Orozco Modesto, Mallol Josefa, Lluís Carme, Canela Enric I., McCormick Peter J., Franco Rafael, et al. , FASEB J, 2013 Mar, Volume 27, p.1048-61, (2013)

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH, Portella, Guillem, Terrazas Montserrat, Villegas Núria, González Carlos, and Orozco Modesto , Angewandte Chemie International Edition, Volume 54, p.10488–10491, (2015)

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations, Zeida, Ari, Machado Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Review E, Volume 86, Number 2, p.021903, (2012)

BioSWR–semantic web services registry for bioinformatics., Repchevsky, Dmitry, and Gelpí Josep-Lluis , PLoS One, 2014, Volume 9, p.e107889, (2014)

The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows, Ejarque, J., Andrio P., Hospital Adam, Conejero J., Lezzi D., Gelpi J. L., and Badia R. M. , 2022 IEEE 18th International Conference on e-Science (e-Science), 12/2022, (2022)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluís , Nucleic Acids Res, 05/2022, Volume 50, Issue W1, p.W107, (2022)

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluis , Bioinformatics, 05/2022, Volume 38, Issue 12, p.3303, (2022)

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows, Andrio, Pau, Hospital Adam, Conejero Javier, Jordá Luis, Del Pino Marc, Codó Laia, Soiland-Reyes Stian, Goble Carole, Lezzi Daniele, Badia Rosa M., et al. , Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (2019)

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)

Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent., Ortega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi , Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data., Hospital, Adam, Andrio Pau, Cugnasco Cesare, Codó Laia, Becerra Yolanda, Dans Pablo D., Battistini Federica, Torres Jordi, Goni Ramon, Orozco Modesto, et al. , Nucleic Acids Res, 2016 Jan 4, Volume 44, Issue D1, p.D272-8, (2016)

Benzoderivatives of nucleic acid bases as modified DNA building blocks., Huertas, Oscar, Blas José Ramón, Soteras Ignacio, Orozco Modesto, and F Luque Javier , J Phys Chem A, 2006 Jan 19, Volume 110, p.510-8, (2006)

Backbone FC-H···O hydrogen bonds in 2’F-substituted nucleic acids., Martín-Pintado, Nerea, Deleavey Glen F., Portella Guillem, Campos-Olivas Ramón, Orozco Modesto, Damha Masad J., and González Carlos , Angew Chem Int Ed Engl, 2013 Nov 11, Volume 52, p.12065-8, (2013)

AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions, Arcon, Juan Pablo, Modenutti Carlos P., Avendaño Demian, Lopez Elias D., Defelipe Lucas A., Ambrosio Francesca Alessandra, Turjanski Adrian G., Forli Stefano, and Martí Marcelo A. , Bioinformatics, 2019, Volume 35, Issue 19, p.3836 - 3838, (2019)

An atomistic view to the gas phase proteome., Meyer, Tim, de la Cruz Xavier, and Orozco Modesto , Structure, 2009 Jan 14, Volume 17, p.88-95, (2009)