HexServer

HexServer performs FFT-based protein docking accelerated by graphics processors to predict and rank protein–protein structural orientations for studying molecular interactions.

Key Features:

• FFT-based docking: Uses Fourier transform (FFT)-based correlation techniques for protein docking calculations.
• GPU acceleration and 6D search: Executes six-dimensional (6D) docking on two graphics processors in parallel, enabling typical runs of approximately 15 seconds and up to two orders of magnitude speedup over traditional FFT-based docking methods with similar resolution and scoring functions.
• Prediction output: Generates a ranked list of up to 1,000 docking predictions from two input protein structures provided in PDB format.
• Focused docking: Restricts searches using known binding-site information to focus and accelerate docking calculations.
• Output formats: Provides the top 20 predictions individually and all predicted orientations as a compressed multi-model PDB file.

Scientific Applications:

• Protein–protein interaction modeling: Rapidly explores candidate interaction conformations and potential binding interfaces for structural biology studies.
• High-throughput docking studies: Enables large-scale or time-sensitive docking experiments through GPU-accelerated throughput.
• Structure-based drug discovery: Supports identification of potential therapeutic targets and analysis of molecular binding mechanisms.

Methodology:

Performs FFT-based 6D protein docking using parallel correlation computations on two graphics processors to generate and rank docking orientations.