Fuzzy bar code representations of DNA-protein interactions

Cheminformatics/Bioinformatics :
A Statement of the Problem

Repression of Transcription

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Representations of DNA Structure:
Can we improve on ATCG?

Electron Density-Derived Molecular Descriptors

Molecular Representations

TAE descriptors

"Histograms or wavelet encoding"

"Segment length and point-of..."

DNA surface pixels (“dixels”)

Nucleotide Triplets to “Dixels”

Base pair properties perturbed by flanking base pairs – raw “Dixel” data

Dixels for PIP

PIP

Dixels for BNP

BNP

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What does this tell us?

DNA/Protein Interaction Modeling:
Bioinformatics through QSPR

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Spatially-Resolved Bioinformatics QSPR of Transcription Factors using “Dixels”

CRP Dixel Model and Conserved base-pairs

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Results: ROC Curve for Identification of transcription factor binding sites on DNA

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Observations from 50-bootstrap selected features on CRP binding sites

Conclusions on CRP

Binding to Sigma Factors

Modeling the binding of Sigma Factors