Fragment Clusters
Clusters of fragments extracted from diverses PDB entries.Clusters of fragments extracted from diverses PDB entries.
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Cluster of RNA Fragments
Description
Protein fragments have been, for a long time, an important research subject in bioinformatics, with applications in protein homology modeling, secondary and tertiary structure prediction, study of sequence-structure relationships and drug design. In this study, we developed a repository containing thousands of protein fragments clustered by structural similarity. These fragments are extracted from different protein datasets, which include a large number of peptides from a non-redundant set of monomeric and globular proteins (MGP), a non-redundant dataset of protein-DNA complex interfaces (PDIdb), a database of protein-DNA complexes (PDC), a non-redundant set of trans-membrane (TM) proteins, and a non – redundant set of RNA structures, among others. The database also includes information like sequence conservation, secondary structure and solvent accessibility surface area were calculated for every fragment in the context of the native structure. Finally, a structure-based search method was implemented using the Ultrafast Shape Recognition (USR) algorithm, allowing the user to provide a fragment in PDB format as a query to search in the database. These improvements, in addition to other features like different Jmol visualizations and dynamic searches, make this database a useful tool to explore the growing universe of peptide conformations and to study the sequence-structure-function relationships in proteins.
Method
The clustering method used is De Novo Clustering based on C3', N1, and the COM of the ring attached to the phosphate.