Structural and Computational BiologyMolecular modelling and bioinformatics

Molecular modelling and bioinformatics
<p>Modesto Orozco</p>
Group Leader

ERC Advanced Grant, Professor (Biochemistry and Molecular Biology Dept. - UB)

+34 93 40 37156

Research keywords

Our research focuses on the study of molecular recognition processes of biological significance from methodological and application points of view. The main subjects addressed are the structure of non-standard nucleic acids, the dynamic properties of macromolecules, and protein-ligand and protein-protein recognition.

Methodological aspects

  • Analysis of the effect of solvent in molecular recognition. Continuum methods are compared to analyse explicit solvent simulations.
  • Fine-tuning of the parametrization of molecular dynamics simulations.

Studies on Small Models

  • Theoretical studies of small model systems of large biological impact. This includes, among others, tautomeric and isomerism processes, stacking interactions, salt bridges, hydrogen bonding, cation-π interactions, and general mechanisms of molecular recognition.

Studies on Proteins

  • We study the basis of protein interactions, including those of pharmacological importance. In addition, we develop methods to examine both protein-protein and protein-ligand recognition.
  • We analyse protein flexibility using massive molecular dynamics simulations.

Studies on Nucleic Acids

  • We use molecular dynamics and statistical mechanics to examine anomalous forms of nucleic acids. Particular attention is paid to the study of conformational transitions in DNA, drug-DNA interactions, and the analysis of triple helices and other structures of potential impact in antigene or antisense therapies.

Bioinformatics

  • Data mining of genomic DNA to identify regions with unusual structures or unusual mechanical properties.
  • Development of algorithms for the prediction of the pathological character of single nucleotide polymorphisms.
  • Structural study of alternative splicing in proteins.
Pluta R, Boer DR, Lorenzo-Díaz F, Russi S, Gómez H, Fernández-López C, Pérez-Luque R, Orozco M, Espinosa M and Coll M.
P Natl Acad Sci Usa, 114 (32), E6526-E653 (2017)
Darré L, Ivani I, Dans PD, Gómez H, Hospital A and Orozco M.
J Am Chem Soc, 138 (50), 16355-1636 (2016)
Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G and Coll M.
Sci Rep, 6 20915 (2016)
Sáez MA, Fernández-Rodríguez J, Moutinho C, Sanchez-Mut JV, Gomez A, Vidal E, Petazzi P, Szczesna K, Lopez-Serra P, Lucariello M, Lorden P, Delgado-Morales R, de la Caridad OJ, Huertas D, Gelpí JL, Orozco M, et all.
Genet Med, (2016)
Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí JL, González C, Vendruscolo M, Laughton CA, Harris SA, Case DA and Orozco M.
Nat Methods, 13 (1), 55-8 (2016)
Habibian M, Martínez-Montero S, Portella G, Chua Z, Bohle DS, Orozco M and Damha MJ.
Org Lett, 17 (21), 5416-9 (2015)
Pujol-Pina R, Vilaprinyó-Pascual S, Mazzucato R, Arcella A, Vilaseca M, Orozco M and Carulla N.
Sci Rep, 5 14809 (2015)
Orozco M.
Chem Soc Rev, 43 (14), 5051-66 (2014)
Dans PD, Faustino I, Battistini F, Zakrzewska K, Lavery R and Orozco M.
Nucleic Acids Res, 42 (18), 11304-20 (2014)
Flores O, Deniz Ö, Soler-López M and Orozco M.
Nucleic Acids Res, 42 (8), 4934-46 (2014)
Fenwick RB, Orellana L, Esteban-Martín S, Orozco M and Salvatella X.
Nat Commun, 5 4070 (2014)
Portella G, Battistini F and Orozco M.
Plos Comput Biol, 9 (11), e1003354 (2013)
Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpí JL and Orozco M.
Plos Comput Biol, 9 (12), e1003393 (2013)
Martin-Pintado N, Deleavey GF, Portella G, Campos-Olivas R, Orozco M, Damha MJ and González C.
Angew Chem Int Edit, 52 (46), 12065-8 (2013)
Martín-Pintado N, Yahyaee-Anzahaee M, Deleavey GF, Portella G, Orozco M, Damha MJ and González C.
J Am Chem Soc, 135 (14), 5344-7 (2013)
Sciabola S, Cao Q, Orozco M, Faustino I and Stanton RV.
Nucleic Acids Res, 41 (3), 1383-94 (2013)
Meyer T, Gabelica V, Grubmüler H, and Orozco M
Wires Comput Mol Sci, 3 (4), 408-425 (2013)
D'Abramo M, Castellazzi CL, Orozco M and Amadei A.
J Phys Chem B, 117 (29), 8697-704 (2013)
Sfriso P, Hospital A, Emperador A and Orozco M.
Bioinformatics, 29 (16), 1980-6 (2013)
Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL and Orozco M.
Nucleic Acids Res, 41 (Web Server), W47-55 (2013)
Orozco M.
Phys Life Rev, 10 (1), 29-30, dis (2013)
Gracia E, Farré D, Cortés A, Ferrer-Costa C, Orozco M, Mallol J, Lluís C, Canela EI, McCormick PJ, Franco R, Fanelli F and Casadó V.
Faseb J, 27 (3), 1048-61 (2013)
Raimondi F, Felline A, Portella G, Orozco M and Fanelli F.
J Biomol Struct Dyn, 31 (2), 142-57 (2013)
Chaudhuri R, Carrillo O, Laughton CA, and Orozco M.
J Chem Theory Comput, 8 (7), 2204-14 (2012)
Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, Martínez-Trillos A, Castellano G, Brun-Heath I, Pinyol M, Barberán-Soler S, Papasaikas P, Jares P, Beà S, Rico D, Ecker S, Rubio M, Royo R, Ho V, Klotzle B, Hernández L, Conde L, López-Guerra M, Colomer D, Villamor N, Aymerich M, Rozman M, Bayes M, Gut M, Gelpí JL, Orozco M, Fan JB, Quesada V, Puente XS, Pisano DG, Valencia A, López-Guillermo A, Gut I, López-Otín C, Campo E and Martín-Subero JI.
Nat Genet, 44 (11), 1236-42 (2012)
Dans PD, Pérez A, Faustino I, Lavery R and Orozco M.
Nucleic Acids Res, 40 (21), 10668-78 (2012)
García-Fandiño R, Bernadó P, Ayuso-Tejedor S, Sancho J and Orozco M.
Plos Comput Biol, 8 (8), e1002647 (2012)
Utz, N, Meyer, T, Rink, G, Orozco, M and Koslowski, T.
J Phys Chem C, 116 (20), 11278-82 (2012)
Pérez A, Castellazzi CL, Battistini F, Collinet K, Flores O, Deniz O, Ruiz ML, Torrents D, Eritja R, Soler-López M and Orozco M.
Biophys J, 102 (9), 2140-8 (2012)
Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL and Palacín M.
P Natl Acad Sci Usa, 108 (10), 3935-40 (2011)

This group receives financial support from the following sources:

  • Fundación Ramón Areces (Ramón Areces Foundation)
  • Ministerio de Educación y Ciencia (MEC - Spanish Ministry of Science and Education)
  • Fundación BBVA (BBVA Foundation)
  • CIRIT – Generalitat de Catalunya (Interdepartmental Committee for Technological Research and Innovation)(Government of Catalonia)
  • Ministerio de Economía y Competitividad (MINECO)
  • European Commission (EC), Fondo Europeo de Desarrollo Regional (FEDER), "Una manera de hacer Europa"

     

People

Group news & mentions

29 Nov 2017

The Community Research and Development Information Service of the European Union (CORDIS) has echoed the SimDNA project conducted by Modesto Orozco and funded through an ERC Advanced Grant.

<p>Modesto Orozco leads the Molecular modelling and bioinformatics laboratory at IRB Barcelona</p>
15 Nov 2017

The programme “24 Horas”, broadcasted by Radio Nacional de España, has interviewed IRB Barcelona researcher Modesto Orozco, co-organiser of the Barcelona Biomed Conference.

<p>In the image, simulation of a chromatin fiber (MuG consortium)</p>
14 Nov 2017

Various media, including El Progreso, the Diario de Pontevedra and Biotech Spain, have echoed the Barcelona Biomed Conference.

<p>In the image, simulation of a chromatin fiber (MuG consortium)</p>
13 Nov 2017

Genomics is one of the most rapidly evolving areas of biology.

Upcoming events

25 Apr
Aula Fèlix Serratosa, Parc Científic de Barcelona
25 Apr
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Dr. Roland Le Borgne, Group leader, Institute of Genetics & Development of Rennes, France.
26 Apr
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Speaker: Dr. Montserrat Terrazas, Molecular modelling and bioinformatics - Structural & Computational Biology Programme, IRB Barcelona