Développement d'une nouvelle méthode performante de classification des surfaces protéiques d'interaction.
Optimisations et extensions du logiciel MED-SuMo.

Olivia Doppelt-Azeroual 1, 2
1 DSIMB Réunion - Dynamique des Structures et Interactions des Macromolécules Biologiques- Pôle de La Réunion
DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques, UR - Université de La Réunion : UMR_S665
Abstract : Resolved three-dimensional protein structures are a major source of information for understanding protein functional properties. The current explosive growth of publicly available protein structures is producing large volumes of data for computational modelling and drug design methods. A protein function is defined by its interactions with specific partners which are the basis of major biological processes. Comparison and detection of protein binding sites are key steps for annotating structures with functional predictions and are extremely valuable steps in a drug design process.
MED-SuMo is a powerful technology to detect and characterise similar local regions on protein surfaces. Each amino acid residue's potential chemical interactions are represented by specific Surface Chemical Features (SCFs). The MED-SuMo heuristic is based on the representation of binding sites by a graph structure suitable for exploration by an efficient comparison algorithm. My PHD work was divided in three points. (1) Optimisations and extensions of MED-SuMo software which led to the underlining of its interest for structural functional annotation. (2) Implementation and development of a new automated functional binding site classification method: MED-SMA. Two applications on different datasets were made and for each, MED-SMA gathers in the same clusters binding sites known to bind the same kind of ligands. (3) At last, I participated to the implementation of a new fragment-based de novo ligand design protocol based on the combination of MED-SuMo technology with a hybridization procedure.
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Olivia Doppelt-Azeroual. Développement d'une nouvelle méthode performante de classification des surfaces protéiques d'interaction.
Optimisations et extensions du logiciel MED-SuMo.. Sciences pharmaceutiques. Université Paris-Diderot - Paris VII, 2009. Français. ⟨tel-00410506⟩

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