|Welcome to ReadOut:|
|Calculation of Direct and Indirect Readout energy Z-scores for Protein-DNA complexes|
Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Proteins usually recognize specific DNA sequences directly through contact between bases and amino acids (Direct Readout). However, proteins can also recognize a DNA sequence indirectly via specific sequence-dependent DNA conformation (e.g., bending and local geometry of base-pair steps), binding-induced distortion of the DNA (flexibility), water-mediated contacts etc. (Indirect Readout). We have developed methods for quantifying the specificity of direct and indirect readouts based on the statistical analysis of the structures of protein-DNA complexes (Refs. 1-3). The methods are based on the calculations of statistical potentials for base-amino acid interactions and DNA conformation and the sequence-structure threading of DNA sequences to calculate protein-DNA interaction and DNA conformational energies. For Direct Readout, the statistical potential is derived from observed spatial distributions of base-amino acid interactions in a non-redundant data set of Protein-DNA complexes, and protein-DNA interaction energy and Z-score (normalized by standard deviation; a measure of specificity) are calculated. For Indirect Readout, the statistical potential is derived from observed distribution of conformational parameters in the same data set, and DNA confomational energy and Z-scores are calculated.
This server calculates:
(1) The DNA conformational energy and Z-score, and
(2) The direct readout or base-amino acid interaction energy and Z-score for protein-DNA complex structures.
This server may be useful if you want to check the specificity of particular protein-DNA complex.
This server is part of our project for understanding protein-DNA recognition mechanism and for target prediction of transcription factors.
(1) H. Kono and A. Sarai "Structure-based prediction of DNA target sites by regulatory proteins" Proteins 35: 114-131 (1999)
(2) S. Selvaraj, H. Kono and A. Sarai "Specificity of Protein-DNA Recognition Revealed by Structure-Based Potentials: Symmetric/Asymmetric and Cognate/Noncognate Binding" J. Mol. Biol. 322: 907-915 (2002)
(3) M.M. Gromiha, J.G. Siebers, S. Selvaraj, H. Kono and A. Sarai "Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition" J. Mol. Biol. 337: 285-294 (2004)
More references are available Here.
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