PepFun

PepFun provides comprehensive bioinformatics and chemoinformatics analyses for peptide sequence characterization, structural modeling, library design, and protein–peptide interaction studies.

Key Features:

• Sequence Analysis: Calculates sequence characteristics and performs extensive analyses of peptide sequences.
• Structural Modeling: Supports modeling of peptide three-dimensional structures and their interactions with proteins.
• Protein–Peptide Interaction Analysis: Derives multiple structural observables from protein–peptide complexes to study molecular interactions.
• Library Design: Generates random and guided peptide sequence libraries for screening and design campaigns.
• Chemoinformatics Integration: Incorporates RDKit-based chemical informatics functions for peptide-related chemical analyses.
• Bioinformatics Integration: Utilizes BioPython-based functions for sequence analysis and related bioinformatic tasks.
• Modularity: Implements a modular architecture enabling customization of analysis workflows.

Scientific Applications:

• Biomarker Discovery: Supports identification of potential peptide biomarkers through sequence and structural analyses.
• Therapeutic Development: Aids design and screening of therapeutic peptides with specific binding properties.
• Vaccine Research: Facilitates analysis of antigenic subunits and peptide candidates for vaccine development.
• Peptide–Protein Interaction Studies: Enables analysis of peptide binders interacting with protein systems such as MHC class II and Granzyme B protease.

Methodology:

Implemented in Python using BioPython for sequence analysis and RDKit for chemoinformatics; supports modeling of peptide structures and peptide–protein interactions, derivation of structural observables from complexes, and random and guided peptide library design.