Methods for proteomics analysis and molecular design

The contruction of an integrated platform for proteomics studies will make molecular dynamics programs readily available for the study of new medicines and it will permit the development of new programs for querying proteomics databases.,in order to aid the study of protein-protein interaction and protein-DNA interaction, for the prediction of protein structures.

In this context the computing resources needed are significant. The development of dedicated hardware or technology analysis based on Grid computing will lead to a significant progress in scientific and technological terms. Within the ICT department there are significant skills, that combined with specific expertise in other departments can lead to important practical results. For example, the skills in computer graphics and geometric modelling present within the ICT department could contribute to the development of a platform for the study of similarities between multidimensional forms.

Particularly significant projects for the CNR like the project for the studies of new medicines will require an accurate planning of computational resources necessary for the study of docking between proteins and for the libraries of potential ligands. An important role will be played by available skills in the project related to the handling and analysis of 3D data through parallel algorithms. In this area the ICT Department and the Medicine and Molecular Design Department could obtain considerable benefits from a close collaboration on these themes.

Here the development of methods for the prediction of the structure, conformal dynamics and protein activities starting from the sequencing information is of primary importance. In CNR-Bioinformatics project the attention will be focused on the development and application of new computational prediction methods of dynamic structural proprieties and of molecular recognition of peptides and proteins. In particular methods based on combination and optimization of conformal sampling methods in low and high resolution and high-performance calculation will be developed. This project has specific objectives such as the development of methods for protein folding and mis-folding prediction; prediction and characterization of protein self-aggregation mechanisms; development of new molecules to a possible pharmacological activity for mis-folding phenomena control.