Biblio

Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct., Busquets, C, Merinero B, Christensen E, Gelpí Josep-Lluis, Campistol J, Pineda M, Fernández-Alvarez E, Prats J M., Sans A, Arteaga R, et al. , Pediatr Res, 2000 Sep, Volume 48, p.315-22, (2000)

Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct., Busquets, C, Merinero B, Christensen E, Gelpí Josep-Lluis, Campistol J, Pineda M, Fernández-Alvarez E, Prats J M., Sans A, Arteaga R, et al. , Pediatr Res, 2000 Sep, Volume 48, p.315-22, (2000)

Sequential amino acid exchange across b(0,+)-like system in chicken brush border jejunum., Torras-Llort, M, Torrents D, Soriano-García J F., Gelpí J L., Estévez R, Ferrer R, Palacín M, and Moretó M , J Membr Biol, 2001 Apr 1, Volume 180, p.213-20, (2001)

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad., Escaja, Núria, Gelpí Josep-Lluis, Orozco Modesto, Rico Manuel, Pedroso Enrique, and González Carlos , J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (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)

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)

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)

Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity., Marti, Luc, Abella Anna, de la Cruz Xavier, García-Vicente Silvia, Unzeta Mercedes, Carpéné Christian, Palacín Manuel, Testar Xavier, Orozco Modesto, and Zorzano Antonio , J Med Chem, 2004 Sep 23, Volume 47, p.4865-74, (2004)

Functional and structural conservation of CBS domains from CLC chloride channels., Estévez, Raúl, Pusch Michael, Ferrer-Costa Carles, Orozco Modesto, and Jentsch Thomas J. , J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)

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)

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study., Pérez, Alberto, Sponer Jiri, Jurecka Petr, Hobza Pavel, F Luque Javier, and Orozco Modesto , Chemistry, 2005 Aug 19, Volume 11, p.5062-6, (2005)

Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient., Muñoz-Muriedas, Jordi, Perspicace Samantha, Bech Nuria, Guccione Salvatore, Orozco Modesto, and F Luque Javier , J Comput Aided Mol Des, 2005 Jun, Volume 19, p.401-19, (2005)

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)

SAR and 3D-QSAR studies on thiadiazolidinone derivatives: exploration of structural requirements for glycogen synthase kinase 3 inhibitors., Martínez, Ana, Alonso Mercedes, Castro Ana, Dorronsoro Isabel, Gelpí Josep-Lluis, F Luque Javier, Pérez Concepción, and Moreno Francisco J. , J Med Chem, 2005 Nov 17, Volume 48, p.7103-12, (2005)

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)

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)

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)

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management, Meyer, Tim, Ferrer-Costa Carles, Pérez Alberto, Rueda Manuel, Bidon-Chanal Axel, F. Luque Javier, Laughton Charles. A., and Orozco Modesto , Journal of Chemical Theory and Computation, 2006/03/01, Volume 2, Issue 2, p.251 - 258, (2006)

Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives., Huertas, Oscar, Poater Jordi, Fuentes-Cabrera Miguel, Orozco Modesto, Solà Miquel, and F Luque Javier , J Phys Chem A, 2006 Nov 9, Volume 110, p.12249-58, (2006)

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)

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)

Determining promoter location based on DNA structure first-principles calculations., J Goñi, Ramon, Pérez Alberto, Torrents David, and Orozco Modesto , Genome Biol, 2007, Volume 8, p.R263, (2007)

Dynamics of B-DNA on the microsecond time scale., Pérez, Alberto, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)

Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters., Reig, Núria, del Rio César, Casagrande Fabio, Ratera Mercè, Gelpí Josep-Lluis, Torrents David, Henderson Peter J. F., Xie Hao, Baldwin Stephen A., Zorzano Antonio, et al. , J Biol Chem, 2007 May 4, Volume 282, p.13270-81, (2007)

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)

Screening of inhibitors of porcine dipeptidyl peptidase IV activity in aqueous extracts from marine organisms, Pascual, Isel, Lopéz Alí, Gómez Hansel, Chappé Mae, Saroyán Angélika, Gonzalez Yamile, Cisneros Miguel, Charli Jean Louis, and Chávez María de los Ang , Enzyme Microb. Technol., Volume 40, Number {3, SI}, {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, p.414-419, (2007)

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)

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)

8-Amino guanine accelerates tetramolecular G-quadruplex formation., Gros, Julien, Aviñó Anna, de la Osa Jaime Lopez, González Carlos, Lacroix Laurent, Pérez Alberto, Orozco Modesto, Eritja Ramon, and Mergny Jean-Louis , Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)

DNAlive: a tool for the physical analysis of DNA at the genomic scale., J Goñi, Ramon, Fenollosa Carlos, Pérez Alberto, Torrents David, and Orozco Modesto , Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids., Svozil, Daniel, Sponer Judit E., Marchán Ivan, Pérez Alberto, Cheatham Thomas E., Forti F, F Luque Javier, Orozco Modesto, and Sponer Jiri , J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

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)

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)

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)

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)

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)

Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis., Lama, Amrita, Pawaria Sudesh, Bidon-Chanal Axel, Anand Arvind, Gelpí Josep-Lluis, Arya Swati, Martí Marcelo, Estrin Darío A., F Luque Javier, and Dikshit Kanak L. , J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors., Castaño, Tania, Wang Huanchen, Campillo Nuria E., Ballester Sara, González-García Coral, Hernández Javier, Pérez Concepción, Cuenca Jimena, Pérez-Castillo Ana, Martínez Ana, et al. , ChemMedChem, 2009 May, Volume 4, p.866-76, (2009)

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors., Castaño, Tania, Wang Huanchen, Campillo Nuria E., Ballester Sara, González-García Coral, Hernández Javier, Pérez Concepción, Cuenca Jimena, Pérez-Castillo Ana, Martínez Ana, et al. , ChemMedChem, 2009 May, Volume 4, p.866-76, (2009)

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools., Perez, Daniel I., Conde Santiago, Pérez Concepción, Gil Carmen, Simon Diana, Wandosell Francisco, Moreno Francisco J., Gelpí Josep-Lluis, Luque Francisco J., and Martínez Ana , Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (2009)

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools., Perez, Daniel I., Conde Santiago, Pérez Concepción, Gil Carmen, Simon Diana, Wandosell Francisco, Moreno Francisco J., Gelpí Josep-Lluis, Luque Francisco J., and Martínez Ana , Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (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)

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)

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?, Darré, Leonardo, Machado Matias R., Dans Pablo Daniel, Herrera Fernando E., and Pantano Sergio , Journal of Chemical Theory and Computation, Volume 6, Number 12, p.3793–3807, (2010)

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)

Differential stability of 2’F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility., Watts, Jonathan K., Martín-Pintado Nerea, Gómez-Pinto Irene, Schwartzentruber Jeremy, Portella Guillem, Orozco Modesto, González Carlos, and Damha Masad J. , Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)