Biblio

Found 303 results
[ Author(Desc)] Title Year
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K
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)
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)
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)
Molecular basis of substrate-induced permeation by an amino acid antiporter., Kowalczyk, Lukasz, Ratera Mercè, Paladino Antonella, Bartoccioni Paola, Errasti-Murugarren Ekaitz, Valencia Eva, Portella Guillem, Bial Susanna, Zorzano Antonio, Fita Ignacio, et al. , Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
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)
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)
L
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)
Nucleic acid simulations themed issue., Laughton, Charles A., and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
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)
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)
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)
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)
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)
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A hybrid all-atom/coarse grain model for multiscale simulations of DNA, Machado, Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Chemistry Chemical Physics, Volume 13, Number 40, p.18134–18144, (2011)
Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations, Machado, Matias R., Dans Pablo Daniel, and Pantano Sergio , Amino acids, Volume 38, Number 5, p.1571–1581, (2010)
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)
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)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom., Martín-Pintado, Nerea, Yahyaee-Anzahaee Maryam, Deleavey Glen F., Portella Guillem, Orozco Modesto, Damha Masad J., and González Carlos , J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
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)
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)
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)
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)
α1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration, Mendoza, Fernanda, Gómez Hansel, Lluch José M., and Masgrau Laura , ACS Catalysis, 2016/04/01, Volume 6, Issue 4, p.2577 - 2589, (2016)
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)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, et al. , Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
Proteins in the gas phase, Meyer, Tim, Gabelica Valérie, Grubmüller Helmut, and Orozco Modesto , WIREs Computational Molecular Science, Volume 3, p.408-425, (2013)
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)
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)
Visualizing phosphodiester-bond hydrolysis by an endonuclease., Molina, Rafael, Stella Stefano, Redondo Pilar, Gómez Hansel, Marcaida María José, Orozco Modesto, Prieto Jesús, and Montoya Guillermo , Nat Struct Mol Biol, 2015 Jan, Volume 22, p.65-72, (2015)
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)
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)
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?, Morreale, Antonio, de la Cruz Xavier, Meyer Tim, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto , Proteins, 2004 Nov 15, Volume 57, p.458-67, (2004)
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)
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index., Muñoz, J, Barril X, Hernández B, Orozco Modesto, and F Luque Javier , J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)
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)
A hydrophobic similarity analysis of solvation effects on nucleic acid bases., Muñoz-Muriedas, Jordi, Barril Xavier, López José María, Orozco Modesto, and Luque Francisco Javier , J Mol Model, 2007 Feb, Volume 13, p.357-65, (2007)
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)
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease., Muñoz-Ruiz, Pilar, Rubio Laura, García-Palomero Esther, Dorronsoro Isabel, del Monte-Millán María, Valenzuela Rita, Usán Paola, de Austria Celia, Bartolini Manuela, Andrisano Vincenza, et al. , J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)
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Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Nadal-Ribelles, Mariona, Conde Núria, Flores Oscar, González-Vallinas Juan, Eyras Eduardo, Orozco Modesto, de Nadal Eulàlia, and Posas Francesc , Genome Biol, 2012, Volume 13, p.R106, (2012)
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)
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)
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)
A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins., Novoa, Eva Maria, de Moura Manuel Castro, Orozco Modesto, and de Pouplana Lluís Ribas , FEBS Lett, 2010 Jan 21, Volume 584, p.460-6, (2010)
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)
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)
The impact of monovalent ion force field model in nucleic acids simulations., Noy, Agnes, Soteras Ignacio, F Luque Javier, and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (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)

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