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

Novoa, E.M., de Pouplana, L.R. & Orozco, M. Small Molecule Docking from Theoretical Structural Models. Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering 75-95 (2012).

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