Contents

• Proteins

  The proteins in the NuclearDB are collected by mining NCBI's NR database for Nuclear Hormone Receptors. We use hidden Markov models (HMMs) to classify the proteins.

• Alignments

  The alignments in the NuclearDB are created by using position-specific profiles. The use of such profiles allows for high-quality alignments. For each protein family the protein sequences of the classified proteins are aligned by the WhatIf software package as described in

  • L. Oliveira, A.C.M. Paiva, G. Vriend, A common motif in G-protein coupled transmembrane seven helix receptors. J. Comp.-Aid. Mol. Des. 7 (1993) 649-658.

Statistics

The NuclearDB currently contains:

Downloads

You can download the protein family members and class descriptions:

• proteins and families (.tar.gz)
• alignments (.tar.gz)