PepVis

PepVis performs large-scale peptide structure modeling and virtual screening to identify and optimize peptide–protein interactions for peptide therapeutic discovery.

Key Features:

• Integration with open-source tools: Uses ModPep and GROMACS for peptide modeling and optimization and AutoDock Vina, ZDOCK, and AutoDock CrankPep (ADCP) for virtual screening.
• Rescoring and refinement: Employs ZRANK2 for rescoring protein–peptide complexes and FlexPepDock for flexible refinement of large protein–peptide complexes.
• Parallel job execution: Supports parallel execution using GNU parallel to increase computational throughput.
• Automated script generation: Generates automated bash scripts to orchestrate modeling, docking, rescoring, and refinement steps.

Scientific Applications:

• Peptide therapeutic discovery: Enables high-throughput computational screening to identify and prioritize peptide candidates for drug development.
• Protein–peptide interaction analysis: Facilitates exploration and optimization of peptide binding conformations and interaction models with protein targets.

Methodology:

Automated script generation; peptide modeling and optimization with ModPep and GROMACS; virtual screening with AutoDock Vina, ZDOCK, and AutoDock CrankPep (ADCP); rescoring with ZRANK2; flexible refinement with FlexPepDock; parallel execution via GNU parallel; benchmarking and validation using the LEADS-PEP dataset (ModPep + Vina reported to outperform others for near-native detection).