Proteomic and Bioinformatics

Description. The main task of this project is to study new approaches, strategies and capabilities of pattern recognition techniques for improving some aspects in the field of bioinformatics and computational biology. In particular modeling and comparison of proteins 3D structures will be considered. Considering the state of the art, it is scheduled to investigate three particular approaches that are not yet being followed (or just partially). 1) Usage of the generalized 3D Hough transform for protein comparison. The main scope of this topic is to search proteins structural similarities in database (PDB). This could be applied to different levels of protein representation (atomic, secondary structure or geometric 3D surfaces). Let's consider, for example, the secondary representation of a protein (made of Helix and Strand). Every detected "evidence" (say Helix or Strand) votes (with a weighted contribution) for a set of "edition" of the model each one corresponding to a given Helix or Strand of the searched protein. By collecting all the contribution, the edition of the model that gathers sufficient votes, determinates the similarity. Notice that G-Hough transform is a parallel algorithm (elements can vote in parallel, proteins can be compared in parallel ...). This could provide good performances on parallel architectures (like CELL BE processor). 2) Usage of the EGI (Extended Gaussian Images) or CEGI (Complex EGI) for solving proteins surface docking (protein-protein or protein-ligand). The objective here is to find complementary regions. EGI is the histogram of surface orientation represented on the unitary sphere. EGI are computationally simple to evaluate and therefore it is worth verifying if necessary condition for docking applied to EGI are enough selective. The Complex EGI is an enriched version in which the orientation is combined with the distance. The advantages/disadvantages of this different approach will be investigated. 3) Applying mathematical morphology (by Serra-Motheron - also known as "image algebra" for others) for surface modeling. The objective is to develop new computational methods that can be applied also to prediction and validation of protein-protein interactions. Simple operands like dilation or erosion can be applied to protein molecular surface modeling. An application can be a comparative analysis finalized to the individuation of topological regions preserved in different species.


Software.

  • "Protein Segmentation and Surface Analyzer"
  • "E.G.I. Protein Visualizer"

  • Publications.

    Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2011). MORPHOLOGICAL ANALYSIS OF 3D PROTEINS STRUCTURE. In Proceedings of Bioinformatics 2011. Part of BIOSTEC 2011. Roma (IT). Jan 26-29, 2011. (pp. 15-21). ISBN: 978-989-8425-36-2.

    Virginio Cantoni, Alessandro Gaggia, Riccardo Gatti, Luca Lombardi. (2011). GEOMETRICAL CONSTRAINTS FOR LIGAND POSITIONING". In Proceedings of Bioinformatics 2011. Part of BIOSTEC 2011. Roma (IT). Jan 26-29, 2011. (pp. 204-209). ISBN: 978-989-8425-36-2.

    Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2010). "SEGMENTATION OF SES FOR PROTEIN STRUCTURE ANALYSIS". In Proceedings of the 1st International Conference on Bioinformatics. BIOSTEC 2010. Valencia (ES). Jan 20-23, 2009. (pp. 83-89). ISBN/ISSN 978-989-674-019-1.

    Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2010). "PROTEINS POCKETS ANALYSIS AND DESCRIPTION". In Proceedings of the 1st International Conference on Bioinformatics. BIOSTEC 2010. Valencia (ES). Jan 20-23, 2009. (pp. 211-216). ISBN/ISSN 978-989-674-019-1.

    Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2009). "Towards Protein Interaction Analysis through Surface Labeling". In Proceedings of the 15th International Conference of Image Analysis and Processing. ICIAP 2009. Vietri sul Mare (IT). Sep 8-11, 2009. (pp. 604-612). ISBN/ISSN 978-3-642-04145-7.

    Virginio Cantoni, Riccardo Gatti, Luca Lombardi. (2010). "Approaches for Protein Surface Curvature Analysis". Submitted to Pattern Analysis and Applications Journal