• Molecular Modeling

    University of Talca

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Welcome to the group of Professor Julio Caballero, at Universidad de Talca in Chile.

The work of my group includes the application of computational methodologies to study complex biomacromolecular systems, mainly focused to the description of the interactions between proteins and small molecules. We are interested in the analysis and processing of available chemical structures of proteins to generate novel chemical information, with potential applications in the design of novel bioactive compounds. Our applications include docking, molecular dynamics, QSAR, hybrid QM/MM methods, free energy calculations, artificial intelligence, and predictive models.

Our research projects have been mainly oriented to the study of enzyme–inhibitor systems such as protein kinases, proteases, etc. We are also interested in questions about the structures of target proteins, such as potassium channels, the sigma1 receptor, the TRPV-1 channel, etc.

The work of our group is inserted in the fields of computational biochemistry, pharmaceutical modeling, protein structure and function, enzyme reactivity and selectivity, and our contributions are mainly focused to medicinal chemistry topics.

Julio Caballero

Biography

Julio Caballero studied Chemistry at Universidad de La Habana, where he graduated with a Gold Diploma in 2001. In 2002-2004 he worked on protein engineering in the Enzyme Technology Group at Universidad de Matanzas. He began t

Research lines

  • Protein-ligand interactions using protocols including docking, molecular dynamics (MD), QSAR, hybrid calculation methods, pharmacophore modeling, de novo design, virtual screening.
  • Ligand-based molecular modeling (QSAR, pharmacophore modeling, chemoinformatics). Applications to the study of the potency of synthetic bioactive compounds and natural products.
  • Substrate specificity of protein kinases (molecular dynamics and FEP calculations).
  • Catalytic mechanism of phosphofructokinase-2.
  • Catalytic mechanism of arginase.
  • Development of the clustering method Bitclust.
  • Study of the structure of sigma1 and its modulators.
  • Development of the tool ligRMSD for comparing the orientations of congeneric compounds in the binding site of a protein.

Selected publications