Affinity Inspector

macbook with slider image 1_edited-1The Affinity Inspector provides scientists with the necessary tools to study the specificity characteristics of an affinity model in the ADB. Each tool is accessible under the tabs:

1. The Specificity & Structure Viewer allows users to interrogate available crystal structures of homologous proteins while also viewing specificity differences within the family to find the biochemical basis for their differences. A completely configurable Needleman-Wunsch (global) optimal alignment aligns the amino acid sequence from the binding experiment to that of the crystal structure. This tool helps researchers to find the mechanistic cause for specificity differences within a protein family. And with this knowledge, scientists can build novel proteins with desired binding properties.

2.The Dinuc Corrections Viewer displays any dinucleotide dependency corrections to the positional independence model via our Dependencies Sequence Logo. The dinucleotide corrections are sorted in decreasing correction-magnitude order – which locates where in the binding site the positional independence assumption breaks down. Also, corrections that decrease affinity are plotted in red while corrections that increase affinity are plotted in green.

3. The Sequence Energy Landscape (SEL) Viewer visualizes the affinity space of a transcription factor (TF) or RNA-binding protein (RBP) while the highest-affinity sequence undergoes an increasing number of point mutations. Coloring of the surface or curtains reveals any nucleotide affinity biases in the sequence-space.

  • Supports zoom, pan, rotation, and reset
  • Supports both 3D surface and curtains plots
  • K-mers can be labeled by an affinity threshold
  • Supports projection onto 2 axes
  • Supports log scale
  • Supports coloring by nucleotide content
  • Max number of point mutations is configurable

4. The Tetrahedron Viewer plots the specificity at each position in the binding site as a distance from the origin at the center of a 3-dimensional tetrahedron. Each corner of the tetrahedron depicts complete specificity for 1 of the 4 DNA or RNA nucleotides.

  • Supports zoom, pan, rotation, and reset
  • Specificity points are colored by binding site position
  • Supports projection onto all 3 axes
  • Star plot measures the magnitude of specificity

5. The Top 1K Viewer lists the top 1000 highest-affinity binding sites generated by the model with their respective relative affinities and free energies of binding.

6. The Pfam Family Alignment Viewer loads and displays the Pfam alignments between the protein of interest and related homologs within its Pfam protein family.

7. The Details Viewer provides detailed information about the species, protein, and affinity model.