PELE

PELE samples protein-ligand conformational space using heuristic perturbations and minimization to explore potential interaction pathways.

Key Features:

• Efficient Modeling: Generates trial moves via perturbations of both protein and ligand, performs side chain sampling and subsequent global or local minimization, and accepts steps that form stochastic trajectories representing potential interaction pathways.
• Parallel Processing Capability: Executes simulations across multiple processors using the Message Passing Interface (MPI) to run collective or independent trajectories for scalable computation.

Scientific Applications:

• Protein–ligand interaction exploration: Simulates atomic-level protein-ligand interactions to map possible binding events and conformational changes.
• Drug discovery and development: Provides binding-mode hypotheses and potential interaction sites to inform lead optimization and drug design.
• Dynamics and trajectory analysis: Enables exploration of multiple stochastic trajectories to analyze dynamic behaviors in biomolecular systems.

Methodology:

Heuristic generation of trial moves via perturbations of protein and ligand, followed by side chain sampling and global or local minimization; accepted steps form stochastic trajectories; parallel execution managed via Message Passing Interface (MPI).