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.

Capabilities

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.

Additional information

  • See for more details of the methods for  Direct and Indirect Readouts.
  • Complete force field used for the indirect readout is provided Here.
  • Data set of proteins used for the developing force fields in ReadOut Web Sever is provided Here.
  • Help for those less familiar with ideas discussed here is available Here.

  • References

    (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.

    Start ReadOut Calculations by filling up the following form

  • Enter three letter PDB code (lower case) of a protein-DNA complex.
  • (If you want to use your own coordinate file instead, please go to the bottom of this page.)
    For simple query, please press submit button, without making any changes in the rest of this page. For advanced query proceed to make changes and click any of the submit or "Read it Out Now" button in this form.

    Advanced Options:
  • Select the number of random sequences to be generated (to get an energy Z- score). help
  • Enter a DNA sequence for finding energy scores for each possible frame (optional, minimum size 20, maximum size 1000). help


  • Choose a Grid size for direct readout energy calculation. help
  • Choose Box dimensions in x, y and z directions for Direct Readout. help.

    X-range:
    Y-range:
    Z-range:
  • Enter the number of bases to skip from the first DNA-chain.
  • Enter the number of bases to skip from the second DNA-chain.
  • Do you want to see energies of all random sequences on the results page?

    (This may lead to large downloads. Please avoid unless necessary).
    (This option is currently disabled).


    You may use your own coordinate file instead of a PDB code to run readout calculations

    Please upload a coordinate file in PDB format to do so.
    (Maximum file size is 1MB).