SiteBinder

SiteBinder performs multiple superimpositions of protein structural motifs to quantify structural conservation and compare 3D motif geometries across large sets of experimentally determined protein structures.

Key Features:

• Systematic Atom Pairing Search: Implements a systematic search for atom pairings that yield optimal fits and uses quaternion algebra to compute root-mean-square deviation (RMSD).
• Efficient Pairing Reduction: Leverages annotations from the Protein Data Bank (PDB) to reduce the number of evaluated atom pairings, enabling alignments when sequence similarity is low or absent.
• Scalability and Throughput: Supports multiple superimpositions of thousands of protein structural motifs for high-throughput analysis.
• Benchmarking on Large Datasets: Demonstrated capability by superimposing 1000 experimentally determined structures for each of 32 eukaryotic linear motifs.

Scientific Applications:

• Eukaryotic linear motifs (large-scale analysis): Superimposition of 1000 structures for each of 32 eukaryotic linear motifs to assess robustness and efficiency.
• PA-IIL Sugar Binding Sites: Comparison of 61 PA-IIL sugar binding sites containing nine different sugars revealed conserved structural features across variants.
• Zinc Finger Central Motifs: Superimposition of over 300 zinc finger central motifs showed high conservation of the molecular structure surrounding the Zn atom.
• BH3 Domains from Pro-apoptotic Proteins: Superimposition of 12 BH3 domains supported a structural basis for the functional segregation of BH3-only proteins into activators and enablers.

Methodology:

Performs a systematic search for atom pairings, computes RMSD using quaternion algebra, reduces candidate pairings via PDB annotations, and performs multiple superimpositions of extensive motif sets.