Biblio

Found 247 results
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Filters: Author is Modesto Orozco  [Clear All Filters]
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Y
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)
U
On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes, D’Abramo, Marco, Meyer Tim, Bernadó Pau, Pons Carles, Recio Juan Fernánde, and Orozco Modesto , Journal of Chemical Theory and Computation, 2009/11/10, Volume 5, Issue 11, p.3129 - 3137, (2009)
The use of conformationally rigid nucleoside probes to study 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 Symp Ser (Oxf), 2009, p.109-10, (2009)
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models., Ferrer-Costa, Carles, Orozco Modesto, and de la Cruz Xavier , Proteins, 2005 Dec 1, Volume 61, p.878-87, (2005)
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location., Durán, Elisa, Djebali Sarah, González Santi, Flores Oscar, Mercader Josep Maria, Guigó Roderic, Torrents David, Soler-López Montserrat, and Orozco Modesto , Nucleic Acids Res, 2013 Aug, Volume 41, p.7220-30, (2013)
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA, Dans, Pablo D., Faustino Ignacio, Battistini Federica, Zakrzewska Krystyna, Lavery Richard, and Orozco Modesto , Nucleic Acid Research, 09/2014, (2014)
Unique tautomeric properties of isoguanine., Blas, José Ramón, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2004 Jan 14, Volume 126, p.154-64, (2004)
Unique tautomeric and recognition properties of thioketothymines?, Faustino, Ignacio, Aviñó Anna, Marchán Ivan, F Luque Javier, Eritja Ramon, and Orozco Modesto , J Am Chem Soc, 2009 Sep 9, Volume 131, p.12845-53, (2009)
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations, Portella, Guillem, Battistini Federica, and Orozco Modesto , PLoS Comput Biol, 11, Volume 9, p.e1003354, (2013)
Unconventional interactions between water and heterocyclic nitrogens in protein structures., Stollar, Elliott J., Gelpí Josep-Lluis, Velankar Sameer, Golovin Adel, Orozco Modesto, and Luisi Ben F. , Proteins, 2004 Oct 1, Volume 57, p.1-8, (2004)
T
Triplex-forming oligonucleotide target sequences in the human genome., J Goñi, Ramon, de la Cruz Xavier, and Orozco Modesto , Nucleic Acids Res, 2004, Volume 32, p.354-60, (2004)
Triplex formation using oligonucleotide clamps carrying 8-aminopurines., Aviñó, Anna, Grimau Marta G., Alvira Margarita, Eritja Ramon, Gargallo Raimundo, Orozco Modesto, and González Carlos , Nucleosides Nucleotides Nucleic Acids, 2007, Volume 26, p.979-83, (2007)
Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study., Curutchet, C, Salichs A, Barril X, Orozco Modesto, and F Luque Javier , J Comput Chem, 2003 Jan 15, Volume 24, p.32-45, (2003)
Towards a molecular dynamics consensus view of B-DNA flexibility., Pérez, Alberto, Lankaš Filip, F Luque Javier, and Orozco Modesto , Nucleic Acids Res, 2008 Apr, Volume 36, p.2379-94, (2008)
Toward an atomistic description of the urea-denatured state of proteins., Candotti, Michela, Esteban-Martín Santiago, Salvatella Xavier, and Orozco Modesto , Proc Natl Acad Sci U S A, 2013 Apr 9, Volume 110, p.5933-8, (2013)
Toward a consensus view of duplex RNA flexibility., Faustino, Ignacio, Pérez Alberto, and Orozco Modesto , Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics., Rueda, Manuel, Chacón Pablo, and Orozco Modesto , Structure, 2007 May, Volume 15, p.565-75, (2007)
A theoretical view of protein dynamics, Orozco, Modesto , Chem. Soc. Rev., Volume 43, p.5051-5066, (2014)
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism., Crespo, Alejandro, Martí Marcelo A., Kalko Susana G., Morreale Antonio, Orozco Modesto, Gelpí Josep-Lluis, F Luque Javier, and Estrin Darío A. , J Am Chem Soc, 2005 Mar 30, Volume 127, p.4433-44, (2005)
Theoretical study of the mechanisms of substrate recognition by catalase., Kalko, S G., Gelpí Josep-Lluis, Fita I, and Orozco Modesto , J Am Chem Soc, 2001 Oct 3, Volume 123, p.9665-72, (2001)
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA., Cubero, Elena, F Luque Javier, and Orozco Modesto , Biophys J, 2006 Feb 1, Volume 90, p.1000-8, (2006)
Theoretical study of the guanine –> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes., Spacková, Nad’a, Cubero Elena, Sponer Jiri, and Orozco Modesto , J Am Chem Soc, 2004 Nov 10, Volume 126, p.14642-50, (2004)
Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water., Noy, Agnes, Pérez Alberto, Laughton Charles A., and Orozco Modesto , Nucleic Acids Res, 2007, Volume 35, p.3330-8, (2007)
Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces., J Blas, Ramón, Márquez Manuel, Sessler Jonathan L., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2002 Oct 30, Volume 124, p.12796-805, (2002)
Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment., Ribas, Jordi, Cubero Elena, F Luque Javier, and Orozco Modesto , J Org Chem, 2002 Oct 4, Volume 67, p.7057-65, (2002)
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex., Cubero, Elena, Abrescia Nicola G. A., Subirana Juan A., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2003 Nov 26, Volume 125, p.14603-12, (2003)
Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site?, Soliva, Robert, Almansa Carmen, Kalko Susana G., F Luque Javier, and Orozco Modesto , J Med Chem, 2003 Apr 10, Volume 46, p.1372-82, (2003)
Theoretical methods for the simulation of nucleic acids., Orozco, Modesto, Pérez Alberto, Noy Agnes, and F Luque Javier , Chem Soc Rev, 2003 Nov, Volume 32, p.350-64, (2003)
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems., Orozco, Modesto, and F. Luque Javier , Chem Rev, 2000 Nov 8, Volume 100, p.4187-4226, (2000)
Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution., García-Fandiño, Rebeca, Granja Juan R., D’Abramo Marco, and Orozco Modesto , J Am Chem Soc, 2009 Nov 4, Volume 131, p.15678-86, (2009)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility., Noy, Agnes, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2008 Mar 19, Volume 130, p.3486-96, (2008)
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)
Target flexibility: an emerging consideration in drug discovery and design., Cozzini, Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., et al. , J Med Chem, 2008 Oct 23, Volume 51, p.6237-55, (2008)
S
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks., Stein, Amelie, Rueda Manuel, Panjkovich Alejandro, Orozco Modesto, and Aloy Patrick , Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA., Lavery, Richard, Zakrzewska Krystyna, Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dixit Surjit, Jayaram B, Lankaš Filip, Laughton Charles, et al. , Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)
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)
Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Martínez-Montero, Saúl, Deleavey Glen F., Dierker-Viik Arden, Lindovska Petra, Ilina Tatiana, Portella Guillem, Orozco Modesto, Parniak Michael A., González Carlos, and Damha Masad J. , The Journal of Organic Chemistry, 2015/03/20, Volume 80, Issue 6, p.3083 - 3091, (2015)
Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams., Soteras, Ignacio, Lozano Oscar, Escolano Carmen, Orozco Modesto, Amat Mercedes, Bosch Joan, and F Luque Javier , J Org Chem, 2008 Oct 3, Volume 73, p.7756-63, (2008)
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer., Dršata, Tomáš, Pérez Alberto, Orozco Modesto, Morozov Alexandre V., Sponer Jiřĺ, and Lankaš Filip , J Chem Theory Comput, 2013, Volume 9, p.707-721, (2013)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid., Noy, Agnes, Pérez Alberto, Márquez Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Structure of triplex DNA in the gas phase., Arcella, Annalisa, Portella Guillem, Ruiz Maria Luz, Eritja Ramon, Vilaseca Marta, Gabelica Valérie, and Orozco Modesto , J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane., Fort, Joana, de la Ballina Laura R., Burghardt Hans E., Ferrer-Costa Carles, Turnay Javier, Ferrer-Orta Cristina, Usón Isabel, Zorzano Antonio, Fernandez-Recio Juan, Orozco Modesto, et al. , J Biol Chem, 2007 Oct 26, Volume 282, p.31444-52, (2007)
Structure and properties of DNA in apolar solvents, Arcella, Annalisa, Portella Guillem, Collepardo-Guevara Rosana, Chakraborty Debayan, Wales David J., and Orozco Modesto , J Phys Chem B, 2014 Jul 24, Volume 118, p.8540-8, (2014)
Structure and Dynamics of Oligonucleotides in the Gas Phase, Arcella, Annalisa, Dreyer Jens, Ippoliti Emiliano, Ivani Ivan, Portella Guillem, Gabelica Valérie, Carloni Paolo, and Orozco Modesto , Angewandte Chemie International Edition, 01/2015, Volume 54, p.467–471, (2015)
The structure and dynamics of DNA in the gas phase., Rueda, Manuel, Kalko Susana G., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)

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