ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Small-angle X-ray scattering (SAXS) filtering enhances protein docking results.
• Current SAXS filtering is computationally intensive, processing millions of conformations sequentially.
• Fast Manifold Fourier Transform (FMFT) enables rapid energy evaluation for protein interactions.

Purpose of the Study:

• To develop a novel algorithm for massively parallel SAXS computation.
• To accelerate the SAXS filtering step in protein docking protocols.
• To enable exploration of the conformational space of interacting proteins.

Main Methods:

• Developed FMFT-SAXS, a novel algorithm leveraging FMFT for SAXS calculations.
• Exploited the convolutional nature of the SAXS calculation function.
• Applied the algorithm to accelerate SAXS filtering in the ClusPro docking server.

Main Results:

• FMFT-SAXS computes SAXS profiles for millions of conformations in minutes.
• Achieved 1-2 orders of magnitude speedup in SAXS filtering without accuracy loss.
• Validated the approach on benchmark datasets and experimental data.

Conclusions:

• FMFT-SAXS significantly accelerates SAXS-based filtering in protein docking.
• The method enables efficient exploration of protein complex conformational landscapes.
• The algorithm is available via the ClusPro server and as an open-source library.