Molecular Modelling and Bioinformatics

Overview: 

MMB GroupOur 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.

RESEARCH DIRECTOR

Orozco López, Modesto

Objectives: 

Methodologic aspects

  • Analysis of the influence of solvent in molecular recognition. Continuum methods are being compared to analysis of 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-ð 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. Methods are being developed to understand both protein-protein and protein-ligand recognition.
  • Protein flexibility is being analysed using massive molecular dynamics simulations

Studies on Nucleic Acids


  • Molecular dynamics and statistical mechanics to study 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.

Massive Genomic Analysis


  • Datamining of genomic DNA to find regions with inusual 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.
Additional Information: 

Further information: http://mmb.pcb.ub.es

PEOPLE

PUBLICATIONS AND COMMUNICATIONS

2012

Arcella A, Portella G, Ruiz ML, Eritja R, Vilaseca M, Gabelica V, Orozco M. Structure of triplex DNA in the gas phase. Journal of the American Chemical Society. 2012 ;134(15):6596-606.
Novoa EM, de Pouplana LR, Orozco M. Small Molecule Docking from Theoretical Structural Models. Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering. 2012 :75-95 .

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