Modesto Orozco

Modesto Orozco's picture
Real name: 
Full name: 
Modesto Orozco
Contact e-mail: 
modesto@mmb.pcb.ub.es
Status: 
Group leader
Research interests: 

Graduate (M.Sc.) in Chemistry from the Universitat Autònoma de Barcelona (1985). PhD in Biochemistry from the same university (1990). Pre-Doctoral research fellow of the Spanish MEC. Departament de Bioquímica - Universitat de Barcelona (1987-1989). Assistant Professor of Biochemistry at the same university (1989-1990). Professor of Biochemistry and Molecular Biology. Departament de Bioquímica. Universitat de Barcelona. 1991-2001. Invited Scientist. Department of Chemistry. Yale University 1991-1993. Full Professor of Biochemistry and Molecular Biology. Departament de Bioquímica. Universitat de Barcelona 2002-present. Director Molecular Modeling and Bioinformatic Unit. Parc Cientific de Barcelona 2001-present. Director of Life Sciences Department Barcelona Supercomputing Center 2004-present. Director of the Joint IRB-BSC research program in Computational Biology 2006-present.

Counselor of the International Society of Quantum Biology and Pharmacology. Coordinator of the Catalan Network of Bioinformatics. Coordinator of the Spanish Network of Molecular Modelling and Chemoinformatics. Coordinator of the Group of Theoretical Molecular Biology of the Spanish Society of Biochemistry and Molecular Biology. Member of different Advisory Commitees. Advisory editor of Theoretical Chemistry Accounts: Theory, Computation and Modeling. Member of the Editorial board of Journal of Computational Chemistry. Member of the Editorial board of Journal of Chemical Theory and Computation. Associated Editor Wiley Interdisciplinary Reviews in Computational Sciences.

Research Interest:

SCRF Methods: We are contributing to the development of new SCRF methods based on the Polarizable Continuum Model of Pisa's group. We are trying to extend the use of these methods to different solvents. We are also developing alternative quasi-classical versions of the method able to work with large systems, coupled to Monte Carlo or molecular dynamics techniques. Finally, our interest is also focused on the extension of the SCRF methods to modeling studies.

QM/MM Methods: We are extending the GMIP(p) approach as a new effective Hamiltonian for QM/MM calculations of large systems. We are trying to optimize the GMIP(p), both from the functional and computational viewpoints. The objective here is to implement GMIP(p) into both Monte Carlo and molecular dynamics frameworks.

Studies on Small Models: We have made several 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- interactions, and general mechanisms of molecular recognition.

Studies on Proteins: We are interested in the understanding of the basis of protein interactions, including those of pharmacological importance. We have also made several studies on very basic aspects of enzymatic reactivity, protein folding and docking.

Studies on Nucleic Acids: We are using molecular dynamics and statistical mechanics to study anomalous or stressed 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. Special effort is made on the determination of physical basis of epigenetic mechanisms and nucleosome positioning.

Bioinformatics:

  • Datamining of genomic DNA to find regions with unusual structures or unusual mechanical properties.
  • Development of algorithms for the prediction of the pathological character of single nucleotide polymorphisms.
  • Determination of regulatory regions of DNA.

References

  1. nucleR: a package for non-parametric nucleosome positioning.,
    Flores, Oscar, and Orozco Modesto
    , Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)