Thermodynamic database for protein-nucleic acid interactions (ProNIT).
BACKGROUND
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 (K(d)), association constant (K(a)), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), heat capacity change (DeltaC(p)), 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.


BACKGROUND
ProNIT is freely accessible at the URL http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html.
Prabakaran
P
P
RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
An
J
J
Gromiha
M M
MM
Selvaraj
S
S
Uedaira
H
H
Kono
H
H
Sarai
A
A
D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D019295:Computational Biology; D003198:Computer Simulation; D004268:DNA-Binding Proteins; D030541:Databases, Genetic; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D009875:Operator Regions, Genetic; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D009696:Nucleic Acids; D011506:Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins