ABSTRACT
The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.
Subject(s)
DNA-Binding Proteins/chemistry , DNA/chemistry , Databases, Protein , RNA-Binding Proteins/chemistry , RNA/chemistry , Internet , Nucleic Acid Conformation , Protein Structure, Tertiary , Software , User-Computer Interface , Water/chemistryABSTRACT
We studied the distribution of 1-7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-represented words. The method described by Karlin et al. has the strongest predictive power compared to other methods. Using this method we identified over- and under-represented words consistent within a large array of taxonomic groups. Some of those words have not yet been described as exclusive. For example, CGCG is over-represented in CG-deficient organisms. We also describe exceptions for widely known exclusive words, such as CG and TA.
