PepPro

PepPro provides a nonredundant benchmark dataset of experimentally determined peptide–protein complex structures for evaluating and improving peptide–protein computational docking algorithms.

Key Features:

• Nonredundant benchmark dataset: Contains 89 experimentally determined peptide–protein complex structures.
• Peptide length range: Peptides span 5 to 30 amino acids in sequence length.
• Secondary-structure diversity: Includes peptides exhibiting helix, partial helix, helix–β-sheet combinations, binding-induced β-sheets, self-folding β-sheets, and coil structures.
• Unbound protein structures: Provides unbound protein structures for 58 complexes to enable assessment of conformational changes during binding.
• Benchmarking purpose: Specifically curated to evaluate and enhance peptide–protein computational docking algorithms.

Scientific Applications:

• Docking algorithm benchmarking: Benchmark and evaluate peptide–protein computational docking algorithms using experimentally determined complex structures.
• Conformational-change assessment: Assess docking methods' ability to handle receptor conformational changes using the 58 unbound protein structures.
• Conformational diversity testing: Test docking performance across diverse peptide secondary structures and lengths (5–30 amino acids).
• Method development: Support development and refinement of peptide docking methodologies.

Methodology:

Compilation of 89 experimentally determined peptide–protein complex structures with annotated peptide secondary-structure motifs and inclusion of 58 corresponding unbound protein structures.