Bioinformatics Vol. 17 no. 11 2001
Pages 1027-1034
© 2001 Oxford University Press
Thermodynamic database for protein–nucleic acid interactions (ProNIT)
1 RIKEN Tsukuba Institute, 3-1-1 Koyadai,
Tsukuba, Ibaraki 305-0074, Japan
2 Department of Chemistry, University of
Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, USA
Received on December 8, 2000
; revised on April 20, 2001
; accepted on April 20, 2001
Motivation: Protein–nucleic acid interactions are fundamental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein–nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have developed a Thermodynamic Database for Protein–Nucleic Acid Interactions (ProNIT).
Results: We have collected experimentally observed binding data
from the literature. ProNIT contains several important thermodynamic
data for protein–nucleic acid binding, such as dissociation
constant (Kd), association constant
(Ka), Gibbs free energy change
(
G), enthalpy change (H), heat capacity
change (Cp), experimental
conditions, structural information of proteins, nucleic acids and
the complex, and literature information. These data are integrated
into a relational database system together with structural and
functional information to provide flexible searching facilities by
using combinations of various terms and parameters. A www interface
allows users to search for data based on various conditions, with
different display and sorting options, and to visualize molecular
structures and their interactions.
Availability: ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.
Contact: sarai{at}rtc.riken.go.jp
* To whom correspondence should be addressed.
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