DBAASP

DBAASP provides a curated database of antimicrobial peptides with amino acid sequences, chemical modifications, three-dimensional structures, bioactivities, and toxicities to support peptide design and antimicrobial research.

Key Features:

• Content statistics: DBAASP v3 contains over 15,700 entries, including more than 14,500 monomeric peptides and nearly 400 homo- and hetero-multimers, with monomeric AMPs comprising over 12,000 synthetic, ~2,700 ribosomally synthesized, and ~170 non-ribosomally synthesized peptides.
• Sequence and chemical data: Detailed amino acid sequences and chemical modifications are provided for database entries.
• Structural data: Three-dimensional structures are included for entries, with over 400 entries linked to experimentally determined structures in the Protein Data Bank.
• Bioactivity and toxicity data: Experimental bioactivities and toxicity measurements are recorded for peptides.
• Multifactor analysis: A multifactor analysis tool examines relevant physicochemical properties of peptides.
• Automated structure modeling: An automated structure-modeling pipeline is used to generate structural models for database peptides.
• Molecular dynamics (MD) simulations: MD simulations and generated MD trajectories and related analyses are available for over 3,200 peptides.

Scientific Applications:

• Peptide design and optimization: Data and multifactor analyses support design and optimization of novel antimicrobial peptides with improved properties such as therapeutic index.
• Structure–function analysis: Three-dimensional structures and MD trajectories enable structure–function investigations of antimicrobial peptides.
• Bioactivity and toxicity assessment: Aggregated experimental bioactivity and toxicity data facilitate comparative analyses of peptide efficacy and safety.
• Integration with experimental structures: Links to Protein Data Bank entries enable correlation of modeled and experimental peptide conformations.

Methodology:

Multifactor analysis of physicochemical properties, an automated structure-modeling pipeline, and molecular dynamics (MD) simulations producing MD trajectories and related analyses, with links to Protein Data Bank experimental structures.