ProtNA-ASA data base: new version including information about electrostatic potential of DNA minor groove
Abstract
Background: In the past decades, the rapid development of molecular biology has led to a generation of an unprecedented amount of biological data obtained by the scientific community. Therefore, there is a significant and unmet need to store, process, and make sense of such a vast amount of data. There are currently available a number of databases, that cover different fields of molecular biology.
Objectives: In this paper, we describe Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area, ProtNA-ASA, http://www.ire.kharkov.ua/ProtNA-ASA/index.php. The main aim of ProtNA-ASA is to provide quick and convenient access to structural information about DNA and protein-DNA complexes, that can be used for comprehensive study of protein-DNA recognition.
Materials and Methods: ProtNA-ASA database comprise information based on X-ray or NMR structures derived from Nucleic Acids Data Bank: 973 structures of protein-DNA complexes, 129 structures of naked А- and 403 of B-DNA ones; following structural parameters for each structure: conformational DNA parameters calculated with the 3DNA/CompDNA analyzer; DNA accessible surface area calculated using the modified algorithm of Higo and Go; DNA electrostatic potential calculated with DelPhi package.
Results: The recent update of ProtNA-ASA includes the electrostatic potential of the DNA minor groove since it plays an essential role in the indirect protein-DNA recognition process. The update also includes an advanced search, which serves to ease the use of the database and contribute to a more accurate structure selection. Advanced search allows finding structures by PDB/NDB ID, citation, length and sequence of a protein or DNA chain, type of structure, method of structure obtaining and resolution. All these queries can be used in different combinations with and/or statements.
Conclusion: The combination of structural information and physical characteristics from the ProtNA-ASA database is particularly useful to scientists studying the indirect readout, that based on DNA deformability. The detail analyzes of protein-DNA complexes and mechanisms of protein-DNA recognition is essential for implications in understanding cellular processes, DNA metabolism, transcriptional regulation, and developing therapeutic drugs.
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References
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