Sequence -- Structure Relation in Proteins

Introduction Prediction of protein three-dimensional structures constitutes a major scientific stake. However, it remains difficult even though it is established that the information needed to specify the complex 3D structure of a protein is contained in its amino acid sequence. Our goal is to analyze protein structures at a local level since protein local structural information is encoded to an extent in local amino acid sequences. In our study, we used an unsupervised clustering method called "Hybrid Protein Model" (HPM) to perform the compression of a nonredundant protein structure databank into a library of overlapping 3D structural fragments [1]. The library obtained is composed of a limited number of structural classes grouping together fragments sharing similar local structures. These classes are characterized by average structural prototypes and are representative of all local folds observed in the protein structure databank. From this library, we analyzed the relation betwee