About the NBDB
Database of sequence-structure profiles with nucleotide-containing and cofactor binding function.
More information about the terminology and database usage is provided in Help and Tutorial section.
Statistics
The database contains 249 sequence profiles of EFLs interacting with different parts of 24 nucleotide-containing ligands and relevant cofactors.
Based on the SCOP classification, representatives of EFLs are found in 74 folds, 84 superfamilies, and 195 families, respectively.
Version and History
Last updated September 20, 2015.- Added cyclic ligands: cAMP, c-di-AMP
- Added PLP, GMP and c-GMP ligands
Authors and contact information
Zejun Zheng (A*STAR) - Data collection and web, supportAlexander Goncearenco (currently at NCBI, NIH) - Methodology development and software
Igor N. Berezovsky (A*STAR) - PI
License
Free for academic, commercial and non-commercial use.References
Cite this database as:Methodology described in:
- Goncearenco, A. & Berezovsky, I.N. 2015. Protein function from its emergence to diversity in contemporary proteins. Physical Biology 12, 045002.
- Goncearenco, A. & Berezovsky, I.N. 2012. Exploring the evolution of protein function in Archaea. BMC Evol Biol 12, 75.
- Goncearenco, A. & Berezovsky, I.N. 2011. Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. Bioinformatics 27, 2368-2375.
- Goncearenco, A. & Berezovsky, I.N. 2010. Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics 26, i497-i503.
Acknowledgements
Built with:- Python, Flask, d3.js, ChemDoodle, JMol, Weblogo
NBDB uses PoseView generated 2D images from the PDB.
Funding:
- Bioinformatics Institute (BII), A*STAR Singapore