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.
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)
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, López-Doriga A, Milà M, Perez-Jurado LA, Pineda M, Armstrong J, Lázaro C and Esteller M.
Genet Med, (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

<p>Examples of computationally designed proteins made of curved beta-sheets and helices forming cavities with different sizes and shapes (E.Marcos, IRB Barcelona-UW)</p>
16 Jan 2017

The local newspaper “La Mañana Diari de Ponent” has echoed a computational study of proteins performed by an international team led by the University of Washington (UW) in Seattle.

<p>Examples of computationally designed proteins made of curved beta-sheets and helices forming cavities with different sizes and shapes (E.Marcos, IRB Barcelona-UW)</p>
13 Jan 2017

An international team of scientists led by the University of Washington (UW) in Seattle has deciphered key rules that govern how proteins form pocket-like structures that are essential for many key

<p>Eadweard Muybridge's pictures of a galloping horse enabled detailed analysis of animals and humans in motion. Today's protein research is faced with a similar situation when trying to understand how proteins move. (L. Orellana)</p>
5 Sep 2016

Proteins are large molecules that carry out all basic cell functions.

<p>11 young scientists will learn about proteins, lab techniques and bioinformatics at IRB Barcelona</p>
21 Jul 2016

Sixty-six youngsters (aged between 16 and 19) from around the world with a passion for science are spending July in research centres around Catalonia as part of the new programme called Bar

Upcoming events

22 Feb
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Silvia Zorilla, CIB-CSIC
22 Feb
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Julián Cerón Madrigal, PhD - Bellvitge Biomedical Research Institute, IDIBELL
23 Feb
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Toni Celià-Terrassa, PhD. Department of Molecular Biology, Princenton University, NJ (USA)