TFmodellerServiceService

TFmodellerServiceService models protein–DNA interactions by homology to predict binding interfaces and generate structural coordinates for studies of transcriptional regulation.

Key Features:

• Homology-Based Modeling: Scans a query protein sequence against a library of experimentally determined protein–DNA complexes from the Protein Data Bank (PDB) to identify templates via homologous relationships.
• Comparative Modeling: Constructs comparative structural models of protein–DNA interfaces using identified homologous templates.
• Comprehensive Outputs: Produces an evolutionary contact matrix, a schematic representation of the predicted binding interface, and atomic coordinates of the modeled protein–DNA complex.
• Regularly Updated Template Library: The library of protein–DNA complexes used for template identification is updated weekly.

Scientific Applications:

• Transcriptional Regulation Studies: Provides structural models to analyze protein–DNA interactions relevant to gene expression control.
• Interface Prediction: Predicts binding interfaces for proteins lacking experimental complex structures.
• Structural Analysis and Validation: Supplies atomic coordinates and contact matrices to support downstream structural analyses and validation experiments.

Methodology:

Scans a protein sequence against a PDB-derived library of protein–DNA complexes, identifies suitable templates by homology, applies comparative modeling techniques to construct protein–DNA interface models, and outputs an evolutionary contact matrix, interface schematic, and atomic coordinates.