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Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
| Content Provider | Open Access Library (OALib) |
|---|---|
| Author | Elena Zotenko Dianne P. O'Leary Teresa M. Przytycka |
| Abstract | In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods.The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests.The extensive collection of protein sequence and structure information has resulted in the creation of numerous classification resources for organizing proteins [1]. Two main structure-based classification databases, SCOP [2] and CATH [3], combine sequence, structural, and functional information to provide a hierarchical classification of known protein structures in the Protein Data Bank (PDB) [4]. In the SCOP database, for example, proteins are organized into a four-level hierarchy: class, fold, super-family, and family. Members of the same family group share a clear common evolutionary origin, supported either by significant sequence similarity or significant structural and functional similarity. The families are grouped into super-families based on structural or functional similarity that suggest a probable common evolutionary origin. The fold level groups proteins based on the arrangement of major secondary structure elements. And finally the class level groups proteins according to their secondary structure |
| ISSN | 14726807 |
| Journal | BMC Structural Biology |
| DOI | 10.1186/1472-6807-6-12 |
| Publisher | BioMed Central |
| Publisher Date | 2006-01-01 |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
| Subject | Structural Biology |
