Overview of NuRISITE
The unified nomenclature system for the nuclear receptor superfamily was used to divide nuclear receptors into 5 subfamilies and 24 groups. For each group, the protein sequences of all the published PDB structures were aligned to the pre-selected representative sequence of the cluster. The pairwise alignments within the cluster were stacked upon each other to generate a multiple alignment of all sequences relative to the representative. Interactions between protein and ligand atoms are extracted from each NR structure in the PDB. Based on the alignments and the interactions found for individual NRs, consensus interaction sites were constructed for both the LBD and the DBD of the each NR group, providing information on the amino acid positions that are in contact with any ligand within the particular subfamily of receptors.
Given a PDB id, a SWISS_PROT id, or a NCBI accession number for a nuclear receptor, NuRISITE permits the user to determine the interaction sites for the query, and to display the amino acid residues of the consensus interaction site for the relevant subfamily. Given an arbitrary protein sequence, NuRISITE can also be used to identify the subfamily, if any, of nuclear receptors to which the query most likely belongs, and then to predict putative interaction sites based on the alignment with the appropriate sequence.