Biblio

Found 318 results
Author [ Title(Asc)] Year
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P
Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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 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)
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)
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)
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)
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)
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)
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)
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)
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)
N
nucleR: a package for non-parametric nucleosome positioning., Flores, Oscar, and Orozco Modesto , Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)
Nucleotide binding switches the information flow in ras GTPases., Raimondi, Francesco, Portella Guillem, Orozco Modesto, and Fanelli Francesca , PLoS Comput Biol, 2011 Mar, Volume 7, p.e1001098, (2011)
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)
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)
Nucleic acid simulations themed issue., Laughton, Charles A., and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
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)
Nature of minor-groove binders-DNA complexes in the gas phase., Rueda, Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2005 Aug 24, Volume 127, p.11690-8, (2005)
On the nature of DNA hyperchromic effect., D’Abramo, Marco, Castellazzi Chiara Lara, Orozco Modesto, and Amadei Andrea , J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps., Sponer, Jiri, Jurecka Petr, Marchán Ivan, F Luque Javier, Orozco Modesto, and Hobza Pavel , Chemistry, 2006 Mar 20, Volume 12, p.2854-65, (2006)
A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase., Albesa-Jové, David, Mendoza Fernanda, Rodrigo-Unzueta Ane, Gomollón-Bel Fernando, Cifuente Javier O., Urresti Saioa, Comino Natalia, Gómez Hansel, Romero-García Javier, Lluch José M., et al. , Angew Chem Int Ed Engl, 2015 Aug 17, Volume 54, p.9898-902, (2015)
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding., Naganathan, Athi N., and Orozco Modesto , J Am Chem Soc, 2011 Aug 10, Volume 133, p.12154-61, (2011)
NAFlex: a web server for the study of nucleic acid flexibility., Hospital, Adam, Faustino Ignacio, Collepardo-Guevara Rosana, González Carlos, Gelpí Josep-Lluis, and Orozco Modesto , Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
M
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)
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)
Multiple routes to characterize the folding of a small DNA hairpin., Portella, Guillem, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Oct 11, Volume 49, p.7673-6, (2010)
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)
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level, Walther, Jurgen, Dans Pablo D., Balaceanu Alexandra, Hospital Adam, Bayarri Genis, and Orozco Modesto , Nucleic Acids Research, 01/2020, (2020)
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)
MST continuum study of the hydration free energies of monovalent ionic species., Curutchet, Carles, Bidon-Chanal Axel, Soteras Ignaci, Orozco Modesto, and F Luque Javier , J Phys Chem B, 2005 Mar 3, Volume 109, p.3565-74, (2005)
Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer’s disease., Muñoz-Muriedas, J, Lopez J M., Orozco Modesto, and F Luque Javier , Curr Pharm Des, 2004, Volume 10, p.3131-40, (2004)
Molecular Dynamics Study of Oligonucleotides Containing Difluorotoluene, Cubero, Elena, Laughton Charles A., F. Luque Javier, and Orozco Modesto , Journal of the American Chemical Society, Volume 122, p.6891-6899, (2000)
Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins, Barbany, Montserrat, Meyer Tim, Hospital Adam, Faustino Ignacio, D’Abramo Marco, Morata Jordi, Orozco Modesto, and de la Cruz Xavier , PLoS ONE, 2015/03/27, Volume 10, p.e0119978 -, (2015)
Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation., Fradera, Xavier, Márquez Manuel, Smith Bradley D., Orozco Modesto, and F Luque Javier , J Org Chem, 2003 Jun 13, Volume 68, p.4663-73, (2003)
Molecular dynamics simulations: advances and applications., Hospital, Adam, J Goñi Ramon, Orozco Modesto, and Gelpí Josep-Lluis , Adv Appl Bioinform Chem, 2015, Volume 8, p.37-47, (2015)
Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions, Arcon, Juan Pablo, Defelipe Lucas A., Modenutti Carlos P., López Elias D., Alvarez-Garcia Daniel, Barril Xavier, Turjanski Adrián G., and Martí Marcelo A. , Journal of Chemical Information and Modeling, 04/2017, Volume 57, Issue 4, p.846 - 863, (2017)

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