Programas de Investigación
Biología Estructural y Computacional
Modelización molecular y bioinformática
Modesto Orozco
Jefe de Grupo
Professor (Biochemistry and Molecular Biology Dept. - UB)
Tel Oficina : +34 93 40 37156
Tel Lab : +34 93 403 71 55
correo-e : modesto.orozco
irbbarcelona.org
Áreas de interés científico
Centramos nuestra investigación en el estudio de los procesos de reconocimiento celular de importancia biológica tanto desde el punto de vista metodológico como aplicacional. Los temas principales son las estructuras no estándar de los ácidos nucleicos, las propiedades dinámicas de las macromoléculas y el reconocimiento proteína-ligando y proteína-proteína.
Líneas de Investigación
Aspectos metodológicos
- Análisis del efecto del solvente en el reconocimiento molecular. Se comparan métodos continuos y métodos basados en simulaciones con solvente explícito
- Ajuste de la parametrización de simulaciones de dinámica molecular.
Estudios en modelos pequeños
- Estudios teóricos en sistemas modelo pequeños de gran impacto biológico. Incluye, entre otros, procesos tautoméricos e isomerismo, interacciones de apilamiento, interacciones electrostáticas y enlaces de hidrógeno, interacciones π-catión y los mecanismos generales de reconocimiento molecular.
Estudios en proteínas
- Estudiamos la base de las interacciones de las proteínas, incluyendo las de relevancia farmacológica. Por otro lado, desarrollamos métodos para examinar tanto el reconocimiento proteína-proteína como proteína-ligando.
- Analizamos la flexibilidad de la proteína utilizando simulaciones de dinámica molecular.
Estudios en ácidos nucleicos
- Utilizamos dinámica molecular y mecánica estadística para examinar las formas anómalas de los ácidos nucleicos. Centramos una atención especial en el estudio de las transiciones conformacionales en el ADN, las interacciones entre fármacos y el ADN, y el análisis de hélices triples y otras estructuras de impacto potencial en terapias antigénicas y antisens.
Bioinformática
- Análisis de datos sobre el ADN genómico para identificar las regiones con estructuras inusuales o con propiedades mecánicas no convencionales.
- Desarrollo de algorismos para la predicción del carácter patológico de los polimorfismos de nucleótidos simples.
- Estudio estructural de splicing en proteínas.
Financiación
Este grupo recibe financiación de las siguientes instituciones:
- Fundación Ramón Areces
- Ministerio de Educación y Ciencia
- Fundación BBVA
- CIRIT – Generalitat de Catalunya
- Comisión Europea
Más información
Modelización molecular y bioinformática
Effects of local electric fields on the redox free energy of single stranded DNA
D'Abramo M, Orozco M and Amadei A
J Nucleic Acids, 47 (9), 2646-2648 (2011)
A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks
Stein A, Rueda M, Panjkovich A, Orozco M and Aloy P
Structure, 19 (6), 881-889 (2011)
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking
Pons C, Talavera D, de la Cruz X, Orozco M and Fernandez-Recio J
J Chem Inf Model, 51 (2), 370-377 (2011)
Toward a consensus view of duplex RNA flexibility
Faustino I, Pérez A and Orozco M
Biophys J, 99 (6), 1876-1885 (2010)
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data
Pons C, D'Abramo M, Svergun DI, Orozco M, Bernadó P and Fernández-Recio J
J Mol Biol, 403 (2), 217-230 (2010)
Multiple routes to characterize the folding of a small DNA hairpin
Portella G and Orozco M
Angew Chem Int Ed Engl, 49 (42), 7673-7676 (2010)
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
Banás P, Hollas D, Zgarbová Jurecka P, Orozco M, Cheatham TE, Sponer J and Otyepka M
J Chem Theory Comput, 6 (3836), 3849 (2010)
Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily
Raimondi F, Orozco M and Fanelli F
Structure, 18 (3), 402-414 (2010)
The EMBRACE web service collection
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM; INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G and Vriend G
Nucleic Acids Res, 38 (Web Server issue), W683-8. Epub 2010 (2010)
Ensemble Docking from Homology Models
Eva Maria Novoa, Lluis Ribas de Pouplana, Xavier Barril, Modesto Orozco
J Chem Theory Comput, 6 (8), 2547-2557 (2010)
A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins
Novoa EM, Castro de Moura M, Orozco M and Ribas de Pouplana L
FEBS Lett, 584 (2), 460-466 (2010)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
Emperador A, Meyer T and Orozco M
Proteins, 78 (1), 83-94 (2010)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, Singh T, Spackova N and Sponer J
Nucleic Acids Res, 38 (1), 299-313 (2010)
Structural properties of g,t-parallel duplexes.
Aviñó A, Cubero E, Gargallo R, González C, Orozco M, Eritja R.
J Nucleic Acids. (2010)
Approaching Elastic Network Models to Molecular Dynamics Flexibility
Orellana L, Rueda M, Ferrer-Costa C, López-Blanco JR, Chacón P and Orozco M
J Chem Theory Comput, 6, 2910-2923 (2010)
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies
Soteras I, Orozco M and Luque FJ
J Comput Aided Mol Des, 24 (4), 281-291 (2010)
Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.
Watts JK, Martín-Pintado N, Gómez-Pinto I, Schwartzentruber J, Portella G, Orozco M, González C, Damha MJ.
Nucleic Acids Res, 8 (7), 2498-511 (2010)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL and Orozco M
Structure, 18 (11), 1399-1409 (2010)
On the use of low-resolution data to improve structure prediction of proteins and protein complexes
D'Abramo M, Meyer T, Bernadó P, Pons C, Fernández-Recio J and Orozco M
J Chem Theory Comput, 5 (11), 3129-3137 (2009)
Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine
Vázquez-Mayagoitia A, Huertas O, Brancolini G, Migliore A, Sumpter BG, Orozco M, Luque FJ, Di Felice R and Fuentes-Cabrera M
J Phys Chem B, 113 (43), 14465-14472 (2009)
Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution
García-Fandiño R, Granja JR, D'Abramo M and Orozco M
J Am Chem Soc, 131 (43), 15678-15686 (2009)
Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies
Soteras I, Forti F, Orozco M and Luque FJ
J Phys Chem B, 113 (27), 9330-9334 (2009)
FlexServ: an integrated tool for the analysis of protein flexibility
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpí JL and Orozco M
Bioinformatics, 25 (13), 1709-1710 (2009)
An atomistic view to the gas phase proteome
Meyer T, de la Cruz X and Orozco M
Structure, 17 (1), 88-95 (2009)
Nucleic acid simulations themed issue
Laughton CA and Orozco M
Phys Chem Chem Phys, 11 (45), 10541-10542 (2009)
The impact of monovalent ion force field model in nucleic acids simulations
Noy A, Soteras I, Luque FJ and Orozco M
Phys Chem Chem Phys, 11 (45), 10596-10607 (2009)
Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields
Fadrná E, Spacková N, Sarzyñska J, Kocá J, Orozco M, Cheatham III T, Kulinski T and Sponer J
J Chem Theor Comput, 5 (9), 2514-2530 (2009)
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling"
Klamtz A, Mennucci B, Tomasi J, Barone V, Curutchet C, Orozco M and Luque FJ
Acc Chem Res, 42 (4), 489-492 (2009)
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
Velázquez-Muriel JA, Rueda M, Isabel C, Pascual-Montano A, Orozco M and Carazo JM
BMC Struct Biol, 9 (1), 6 (2009)
X-pol potential: An electronic structure-based force field for molecular dynamics simulation of a solvated protein in water
Xie W, Orozco M, Truhlar D and Gao J
J Chem Theor Comput, 5 (3), 459-467 (2009)
Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE and Eritja R
Nucleic Acids Res, 37 (17), 5589-5601 (2009)
Unique tautomeric and recognition properties of thioketothymines?
Faustino I, Aviño A, Marchán I, Luque FJ, Eritja R and Orozco M
J Am Chem Soc, 131 (35), 12845-12853 (2009)
The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer
Saneyoshi H, Mazzini S, Aviñó A, Portella G, González C, Orozco M, Marquez VE and Eritja R
Nucleic Acids Symp Ser, 53, 109-110 (2009)
COCO: A simple tool to enrich the representation of conformational variability in NMR structures
Laughton CA, Orozco M and Vranken W
Proteins, 75 (1), 206-216 (2008)
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
Emperador A, Carrillo O, Rueda M and Orozco M
Biophys J, 95 (5), 2127-2138 (2008)
Interoperability with Moby 1.0--it's better than sharing your toothbrush!
The Biomoby consortium (including Orozco M, Gelpí JL and others)
Brief Bioinform, 9 (3), 220-231 (2008)
Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian
Forti F, Barril X, Luque FJ and Orozco M
J Comput Chem, 29 (4), 578-587 (2008)
Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility
Noy A, Luque FJ and Orozco M
J Am Chem Soc, 130 (11), 3486-3496 (2008)
8-Amino guanine accelerates tetramolecular G-quadruplex formation
Gros J, Aviñó A, Lopez de la Osa J, González C, Lacroix L, Pérez A, Orozco M, Eritja R and Mergny JL
Chem Commun, 7 (25), 2926-2928 (2008)
GRID-MD-A tool for massive simulation of protein channels
Carrillo O and Orozco M
Proteins, 70 (3), 892-899 (2008)
Ab initio study of naphtho-homologated DNA bases
Vázquez-Mayogoita A, Huertas O, Fuentes-Cabrera M, Sumpter BG, Orozco M and Luque FJ
J Phys Chem B, 112 (7), 2179-2186 (2008)
Recent advances in the study of nucleic acid flexibility by molecular dynamics
Orozco M, Noy A and Pérez A
Curr Opin Struct Biol, 18 (2), 185-193 (2008)
DNAlive: a tool for the physical analysis of DNA at the genomic scale
Goñi JR, Fenollosa C, Pérez A, Torrents D and Orozco M
Bioinformatics, 24 (15), 1731-1732 (2008)
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids
Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE 3rd, Forti F, Luque FJ, Orozco M and Sponer J
J Phys Chem B, 112 (27), 8188-8197 (2008)
Induction effects in metal cation-benzene complexes
Soteras I, Orozco M and Luque FJ
Phys Chem Chem Phys, 10 (19), 2616-2624 (2008)
Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams
Soteras I, Lozano O, Escolano C, Orozco M, Amat M, Bosch J and Luque FJ
J Org Chem, 73 (19), 7756-7763 (2008)
Target flexibility: an emerging consideration in drug discovery and design
Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM, Orozco M, Pertinhez TA, Rizzi M and Sotriffer CA
J Med Chem, 51 (20), 6237-6255 (2008)
Towards a molecular dynamics consensus view of B-DNA flexibility
Pérez A, Lankas F, Luque FJ and Orozco M
Nucleic Acids Res, 36 (7), 2379-2394 (2008)
United-atom discrete molecular dynamics of proteins using physics-based potentials
Emperador A, Meyer T and Orozco M
J Chem Theory Comput, 4 (12), 2001-2010 (2008)
Solvation enthalpies of neutral solutes in water and octanol
Bidon-Chanal A, Huertas O, Orozco M and Luque FJ
Theor Chem Acc, 123 (1-2), 11-20 (2008)
Derivation of distributed models of atomic polarizability for molecular simulations
Soteras I, Curutchet C, Bidon-Chanal A, Dehez F, Angyan J, Orozco M, Chipot C and Luque FJ
J Chem Theory Comput, 3 (6), 1901-1913 (2007)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane
Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Usón I, Zorzano A, Fernández-Recio J, Orozco M, Lizarbe MA, Fita I and Palacín M
J Biol Chem, 282 (43), 31444-31452 (2007)
Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent
Ortega JA, Blas JR, Orozco M, Grandas A, Pedroso E and Robles J
Org Lett, 9 (22), 4503-4506 (2007)
Dynamics of B-DNA on the microsecond time scale
Pérez A, Luque FJ and Orozco M
J Am Chem Soc, 129 (47), 14739-14745 (2007)
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water
Noy A, Pérez A, Laughton CA and Orozco M
Nucleic Acids Res, 35 (10), 3330-3338 (2007)
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
Rueda M, Chacón P and Orozco M
Structure, 15 (5), 565-575 (2007)
The (in)dependence of alternative splicing and gene duplication
Talavera D, Vogel C, Orozco M, Teichmann SA and de la Cruz X
PLoS Comput Biol, 3 (3), 375-388 (2007)
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE 3rd, Laughton CA and Orozco M
Biophys J, 92 (11), 3817-3829 (2007)
A procedure for identifying homologous alternative splicing events
Talavera D, Hospital A, Orozco M and de la Cruz X
BMC Bioinformatics, 8, 260-271 (2007)
A consensus view of protein dynamics
Rueda M, Ferrer-Costa C, Meyer T, Pérez A, Camps J, Hospital A, Gelpí JL and Orozco M
Proc Natl Acad Sci USA, 104 (3), 796-801 (2007)
Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution
Blas JR, López-Bes JM, Márquez M, Sessler JL, Luque FJ and Orozco M
Chemistry, 13 (4), 1108-1116 (2007)
Characterization of compensated mutations in terms of structural and physico-chemical properties
Ferrer-Costa C, Orozco M and de la Cruz X
J Mol Biol, 365 (1), 249-256 (2007)
Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family
Soliva R, Gelpi JL, Almansa C, Virgili M and Orozco M
J Med Chem, 50 (2), 283-293 (2007)
A hydrophobic similarity analysis of solvation effects on nucleic acid bases
Muñoz-Muriedas J, Barril X, López JM, Orozco M and Luque FJ
J Mol Model, 13 (2), 357-365 (2007)
Triplex formation using oligonucleotide clamps carrying 8-aminopurines
Aviñó A, Grimau MG, Alvira M, Eritja R, Gargallo R, Orozco M and González C
Nucleosides Nucleotides Nucleic Acids, 26 (8-9), 979-983 (2007)
Continuum analysis of conformational sampling in solution. In Continuum Solvation Models in Chemical Physics: Theory and Application
Orozco M, Marchán I and Soteras I
Mennucci B and Cammi R (Eds), Elsevier, 499-522 (2007)
Determining promoter location based on DNA structure first-principles calculations
Goñi JR, Pérez A, Torrents D and Orozco M
Genome Biol, 8 (12), R263 (2007)
A fast method for the determination of fractional contributions to solvation in proteins
Talavera D, Morreale A, Meyer T, Hospital A, Ferrer-Costa C, Gelpi JL, de la Cruz X, Soliva R, Luque FJ and Orozco M
Protein Sci, 15 (11), 2525-2533 (2006)
Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives
Huertas O, Poater J, Fuentes-Cabrera M, Orozco M, Solà M and Luque FJ
J Phys Chem A, 110 (44), 12249-12258 (2006)
Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model
Curutchet C, Orozco M, Luque FJ, Mennucci B and Tomasi J
J Comput Chem, 27 (15), 1769-1780 (2006)
On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates
Soteras I, Lozano O, Gómez-Esqué A, Escolano C, Orozco M, Amat M, Bosch J and Luque FJ
J Am Chem Soc, 128 (20), 6581-6588 (2006)
G-quadruplexes can maintain their structure in the gas phase
Rueda M, Luque FJ and Orozco M
J Am Chem Soc, 128 (11), 3608-3619 (2006)
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions
Goñi JR, Vaquerizas JM, Dopazo J and Orozco M
BMC Genomics, 7, 63-72 (2006)
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M and Hobza P
Chemistry, 12 (10), 2854-2865 (2006)
Benzoderivatives of nucleic acid bases as modified DNA building blocks
Huertas O, Blas JR, Soteras I, Orozco M and Luque FJ
J Phys Chem A, 110 (2), 510-518 (2006)
Destabilization of quadruplex DNA by 8-aminoguanine
López de la Osa J, González C, Gargallo R, Rueda M, Cubero E, Orozco M, Aviñó A and Eritja R
Chembiochem, 7 (1), 46-48 (2006)
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA
Cubero E, Luque FJ and Orozco M
Biophys J, 90 (3), 1000-1008 (2006)
Data mining of molecular dynamics trajectories of nucleic acids
Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Pérez A, de la Cruz X, López-Bes JM, Pouplana R, Fernandez-Recio J, Luque FJ and Orozco M
J Biomol Struct Dyn, 23 (4), 447-456 (2006)
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N
Bidon-Chanal A, Martí MA, Crespo A, Milani M, Orozco M, Bolognesi M, Luque FJ and Estrin DA
Proteins, 64 (2), 457-464 (2006)
Essential dynamics: a tool for efficient trajectory compression and management
Meyer T, Ferrer-Costa C, Pérez A, Rueda M, Bidon-Chanal A, Luque FJ, Laughton CA and Orozco M
J Chem Theory Comput, 2 (2), 251-258 (2006)
Aromaticity-induced changes in electronic properties of size-expanded DNA bases: Case of xC
Fuentes-Cabrera M, Lipkowski P, Huertas O, Sumpter BG, Orozco M, Luque FJ, Wells JC and Leszczynski J
Int J Quantum Chem, 106 (11), 2339-2346 (2006)
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer's disease
Muñoz-Ruiz P, Rubio L, García-Palomero E, Dorronsoro I, del Monte-Millán M, Valenzuela R, Usán P, de Austria C, Bartolini M, Andrisano V, Bidon-Chanal A, Orozco M, Luque FJ, Medina M and Martínez A
J Med Chem, 48 (23), 7223-7233 (2005)
MST continuum study of the hydration free energies of monovalent ionic species
Curutchet C, Bidon-Chanal A, Soteras I, Orozco M and Luque FJ
J Phys Chem B, 109 (8), 3565-3574 (2005)
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism
Crespo A, Martí MA, Kalko SG, Morreale A, Orozco M, Gelpi JL, Luque FJ and Estrin DA
J Am Chem Soc, 127 (12), 4433-4444 (2005)
Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient
Muñoz-Muriedas J, Perspicace S, Bech N, Guccione S, Orozco M and Luque FJ
J Comput Aided Mol Des, 19 (6), 401-419 (2005)
PMUT: a web-based tool for the annotation of pathological mutations on proteins
Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X and Orozco M
Bioinformatics, 21 (14), 3176-3178 (2005)
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M and Dopazo J
Nucleic Acids Res, 3, 501-505 (2005)
Partition of protein solvation into group contributions from molecular dynamics simulations
Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ and Orozco M
Proteins, 58 (1), 101-109 (2005)
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models
Ferrer-Costa C, Orozco M and de la Cruz X
Proteins, 61 (4), 878-887 (2005)
Donepezil-tacrine hybrid related derivatives as new dual binding site inhibitors of AChE
Alonso D, Dorronsoro I, Rubio L, Muñoz P, García-Palomero E, Del Monte M, Bidon-Chanal A, Orozco M, Luque FJ, Castro A, Medina M and Martínez A
Bioorg Med Chem, 13 (24), 6588-6597 (2005)
Nature of minor-groove binders-DNA complexes in the gas phase
Rueda M, Luque FJ and Orozco M
J Am Chem Soc, 127 (33), 11690-11698 (2005)
Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study
Pérez A, Sponer J, Jurecka P, Hobza P, Luque FJ and Orozco M
Chemistry, 11 (17), 5062-5066 (2005)
Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations
Soteras I, Curutchet C, Bidon-Chanal A, Orozco M and Luque FJ
J Mol Struct Theochem, 727 (1-3), 29-40 (2005)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid
Noy A, Pérez A, Márquez M, Luque FJ and Orozco M
J Am Chem Soc, 127 (13), 4910-4920 (2005)
Exploring the essential dynamics of B-DNA
Pérez A, Blas JR, Rueda M, López-Bes JM, de la Cruz X and Orozco M
J Chem Theory Comput, 1, 790-800 (2005)
Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity
Marti L, Abella A, De La Cruz X, García-Vicente S, Unzeta M, Carpéné C, Palacín M, Testar X, Orozco M and Zorzano A
J Med Chem, 47 (20), 4865-4874 (2004)
Relative flexibility of DNA and RNA: a molecular dynamics study
Noy A, Pérez A, Lankas F, Javier Luque F and Orozco M
J Mol Biol, 343 (3), 627-638 (2004)
Unconventional interactions between water and heterocyclic nitrogens in protein structures
Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M and Luisi BF
Proteins, 57 (1), 1-8 (2004)
The relative flexibility of B-DNA and A-RNA duplexes: database analysis
Pérez A, Noy A, Lankas F, Luque FJ and Orozco M
Nucleic Acids Res, 32 (20), 6144-6151 (2004)
Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes
Spacková N, Cubero E, Sponer J and Orozco M
J Am Chem Soc, 126 (44), 14642-14650 (2004)
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ and Orozco M
Proteins, 57 (3), 458-467 (2004)
Effect of bulky lesions on DNA: Solution structure of a DNA duplex containing a cholesterol adduct
Gómez-Pinto I, Cubero E, Kalko SG, Monaco V, van der Marel G, van Boom JH, Orozco M and González C
J Biol Chem, 279 (23), 24552-24560 (2004)
Functional and structural conservation of CBS domains from CLC chloride channels
Estévez R, Pusch M, Ferrer-Costa C, Orozco M and Jentsch TJ
J Physiol, 557 (Pt2), 363-378 (2004)
Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species
Valenzuela A, Talavera D, Orozco M and de la Cruz X
J Mol Biol, 335 (2), 495-502 (2004)
Triplex-forming oligonucleotide target sequences in the human genome
Goñi JR, de la Cruz X and Orozco M
Nucleic Acids Res, 32 (1), 354-360 (2004)
Unique tautomeric properties of isoguanine
Blas JR, Luque FJ and Orozco M
J Am Chem Soc, 126 (1), 154-164 (2004)
Sequence-based prediction of pathological mutations
Ferrer-Costa C, Orozco M and de la Cruz X
Proteins, 57 (4), 811-819 (2004)
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
Rueda M, Cubero E, Laughton CA and Orozco M
Biophys J, 87 (2), 800-811 (2004)
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives
Aviñó A, Cubero E, González C, Eritja R and Orozco M
J Am Chem Soc, 125 (51), 13127-16138 (2003)
Modelización molecular y bioinformática
© Photos by Gianluca Battista/Massimiliano Minocri
Modesto Orozco
Jefe de Grupo
Professor (Biochemistry and Molecular Biology Dept. - UB)
Tel Oficina : +34 93 40 37156
Tel Lab : +34 93 403 71 55
correo-e : modesto.orozcoirbbarcelona.org
Investigadores Asociados
Agustí Emperador
tel +34 93 40 34707
e-mail: agusti.emperadorirbbarcelona.org
Josep Ll. Gelpí
tel +34 93 40 34707
e-mail: josep.gelpiirbbarcelona.org
Manuel Rueda
tel +34 93 40 37155
e-mail: manuel.ruedairbbarcelona.org
Investigadores Postdoctorales
Andreu Alibés
tel +34 93 40 37155
e-mail: andreu.alibesirbbarcelona.org
Federica Battistini
tel +34 93 40 37155
e-mail: federica.battistiniirbbarcelona.org
Guillem Portella
tel +34 93 40 34707
e-mail: guillem.portellairbbarcelona.org
Nadine Simone Utz
tel +34 93 40 39073
e-mail: nadine.utzirbbarcelona.org
Pablo Ignacio Daniel Dans
tel +34 93 40 37155
e-mail: pablo.dansirbbarcelona.org
Rima Chaudhuri
tel +34 93 40 37155
e-mail: rima.chaudhuriirbbarcelona.org
Robert Soliva
tel +34 93 40 37155
e-mail: robert.solivairbbarcelona.org
Rosana Collepardo
tel +34 93 40 37155
e-mail: rosana.collepardoirbbarcelona.org
Samira Jaeger
tel +34 93 40 37155
e-mail: samira.jaegerirbbarcelona.org
Estudiantes de Doctorado
Annalisa Arcella
tel +34 93 40 37155
e-mail: annalisa.arcellairbbarcelona.org
Elisa Durán
tel +34 93 40 20228
e-mail: elisa.duranirbbarcelona.org
Ignacio Faustino
tel +34 93 40 37155
e-mail: ignacio.faustinoirbbarcelona.org
Ivan Ivani
tel +34 93 40 37155
e-mail: ivan.ivaniirbbarcelona.org
Laura Orellana
tel +34 93 40 37155
e-mail: laura.orellanairbbarcelona.org
Michela Candotti
tel +34 93 40 37155
e-mail: michela.candottiirbbarcelona.org
Oscar Flores
tel +34 93 40 37155
e-mail: oscar.floresirbbarcelona.org
Ozgen Deniz
tel +34 93 40 20228
e-mail: ozgen.denizirbbarcelona.org
Pedro Sfriso
tel +34 93 40 37155
e-mail: pedro.sfrisoirbbarcelona.org
Estudiantes de Máster
Marco Paulo Seco
tel +34 93 40 37155
e-mail: marco.secoirbbarcelona.org
Ayudantes de Investigación
Adam Hospital
tel +34 93 40 37155
e-mail: adam.hospitalirbbarcelona.org
Chiara Lara Castellazzi
tel +34 93 40 20228
e-mail: chiara.castellazziirbbarcelona.org
Floriane Montanari
tel +34 93 40 37155
e-mail: floriane.montanariirbbarcelona.org
José Antonio Alcántara
tel +34 93 40 37155
e-mail: jose.alcantarairbbarcelona.org
Pedro Manuel Martínez
tel +34 93 40 37155
e-mail: pedromanuel.martinezirbbarcelona.org
Asistente Administrativa
Margarita Pedro
tel +34 93 40 37155
e-mail: margarita.pedroirbbarcelona.org
Investigadores Visitantes
Athi Narayanan Naganathan
tel +34 93 40 39073
e-mail: athi.naganathanirbbarcelona.org
Modelización molecular y bioinformática
- 28 Enero 2012
El Periódico de Catalunya
“El Gordo” de la ciencia - 25 Enero 2012
El Periódico de Catalunya
Europa otorga a científicos catalanes siete becas de élite - 25 Enero 2012
La Vanguardia
Europa reconoce a Catalunya como motor de la excelencia científica en España - 24 Enero 2012
ABC
El IRB concentra el 20 por ciento de las becas otorgadas por la UE a España - 24 Enero 2012
Institute News
El IRB Barcelona obtiene el 20% de los proyectos europeos ERC Advanced otorgados a EspañaLos profesores Cayetano González, Angel R. Nebreda y Modesto Orozco han sido premiados con sendas ERC Advanced Grant, los dos primeros en la categoría de Ciencias de la Vida y el último en Ciencias Físicas e Ingeniería.
Sólo el 13% de los investigadores europeos que se han presentado a la convocatoria de 2011 han superado la criba.
Cada proyecto tiene una dotación económica aproximada de dos millones y medio de euros para cinco años.
- 12 Diciembre 2011
Diario Médico
Nuevo paradigma para el hallazgo de fármacos - 12 Diciembre 2011
La Vanguardia
El genoma de la leucemia abre la vía para mejorar el tratamiento - 13 Diciembre 2011
Noticia Científica
Nuevos resultados del Consorcio Español para el Estudio del Genoma de la LeucemiaEl trabajo de investigación, que hace público la revista Nature Genetics, ha estudiado el genoma de cien pacientes con leucemia y ha identificado más de mil nuevos genes mutados en el desarrollo de esta enfermedad
Este estudio supone un gran avance hacia la culminación de los objetivos del Consorcio Español para el Estudio del Genoma de la Leucemia Linfática Crónica
- 26 Octubre 2011
Notícia Institucional
Modesto Orozco obtiene una ERC Advanced Grant, la ayuda por proyecto científico con más prestigio de EuropaEl Consejo Europeo de Investigación otorga las ERC Advanced Grant a un número muy reducido de investigadores senior con una financiación que oscila entre 2 y 3 millones de euros para cinco años.
El proyecto multidisciplinar, premiado dentro de la categoría de Ciencias Físicas e Ingeniería, se ubica en las especialidades de química y biología computacional, biología estructural, biofísica, bioinformática y tendrá aplicaciones directas en diversas áreas de la biomedicina como en regulación de expresión génica y en mecanismos epigenéticos.
- 8 Septiembre 2011
Noticia Científica
Flexibilidad para funcionalidad: el nuevo dogma de la estructura de las proteínas
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