RsiteDB -- RNA binding sites database
What you can do:
Find information about protein binding pockets that interact with RNA nucleotides.
Highlights:
- RsiteDB is a database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases.
- The database consists of a classification of binding sites derived from protein-RNA complexes.
- Each binding site is assigned to a cluster of similar binding sites in other protein-RNA complexes.
- Cluster members share similar spatial arrangements of physico-chemical properties, and can reveal novel similarity between proteins and RNAs with different sequences and folds.
- The clusters provide 3D consensus binding patterns important for protein-nucleotide recognition.
- The database search engine allows two types of useful queries: first, given a PDB code of a protein-RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing.
- The second search query: given an unbound protein structure, RsiteDB can perform an on-line structural search against the constructed database of 3D consensus binding patterns.
- Regions similar to known patterns are predicted to serve as binding sites.
- Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein-RNA interactions at the atomic level of detail.
Keywords:
- RNA nucleotide
- protein binding pocket
- protein structure
- RNA ligand
- protein-RNA interaction
Literature & Tutorials:
This record last updated: 02-20-2009