Omokage search

Omokage search identifies structurally similar macromolecular assemblies in the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) by comparing global shapes using incremental distance rank profiles and aligning matches with Gaussian mixture model fitting (gmfit).

Key Features:

• Shape-Based Search: Identifies similar-shaped structures within PDB and EMDB independent of sequence order or subunit composition.
• Shape Characterization: Uses one-dimensional incremental distance rank profiles to characterize and compare global shapes of macromolecular assemblies.
• Rapid Processing: Performs shape-based searches within approximately one minute.
• Structural Fitting: Uses gmfit (Gaussian mixture model fitting) to align identified structures to the query for structural comparison.

Scientific Applications:

• Macromolecular assembly comparison: Compare protein complexes, viral capsids, and other large biological assemblies based on overall shape rather than sequence.
• Detection of structural motifs and analogs: Identify novel structural motifs and potential functional analogs across species.
• Evolutionary and functional inference: Support inference of evolutionary relationships and functional similarities from shape-based structural similarity.

Methodology:

Compares global shapes using incremental distance rank profiles and fits identified structures onto the query using the gmfit program (Gaussian mixture model fitting) to produce aligned structural representations.