A Classification Procedure for Functional RNA Crystal Structures

HD-RNAS is a classification of functional RNA structures available in PDB. All the RNA Crystallographic structures, NMR structures and Electron Microscopic structures having at least one RNA chain longer than 9 nucleotides are classified in 10 major functional classes. Each class is further classified according to the source organism from which the RNA molecules were isolated and crystallized.
Presently, HD-RNAS v2.0 contains 1060 crystal structures, containing 3066 RNA chains. The proper source organisms of RNA structure colected from sourse organism and other details field . The non-redundant set of structures consists of many PDB entries, indicating the best representative structures from each of the sub-classes based on their resolution and R-factor.

Structural/Functional Classification of 3066 RNA Chains
mRNA    Pseudoknot    Ribonuclease    Riboswitch    Ribozyme    rRNA    snRNA    tarRNA    Tetraloop    tRNA    Unclassified

BPFIND

A Software for detection and analysis of Hydrogen Bonded Base Pairs in a nucleic acid structure. The program looks for at least two hydrogen bonds between two nucleotide bases. This can also detect possible protonated base pairs.

BPFIND Web-server

BPFIND Standalone

Citation : Das J., Mukherjee S., Mitra A., Bhattacharyya D. (2006). Non-canonical base pairs and higher order structures in nucleic acids crystal structure database analysis. J. Biomol. Struct. Dynam. 24, 149–161 [PubMed]

NUPARM

A Software for analysis of nucleic acid structure mainly through different base pair parameters.

NUPARM Web-server

NUPARM Standalone

Citation : Mukherjee S., Bansal M., Bhattacharyya D. (2006). Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J. Comput.Aided Mol.Des. 20 (10-11), 629-645 [PubMed]

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Organism Search process is very similar to that of ID Search. In organism search one can simply query with Genus species or G. species type of query. Only one organism at a time can be search here.

Some well known functional RNA types are pre determined for Functional RNA Search catagory. One has to select the radio button on left of a particular catagory to search that. In case of rRNA/tRNA first select the radio button on left, then select specific type of rRNA/tRNA from dropdown on the right.
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