B-AMP

B-AMP provides a repository of predicted 3D structures of antimicrobial peptides (AMPs) and associated protein–peptide interaction models to support identification and prioritization of anti-biofilm AMP candidates.

Key Features:

• Extensive repository: B-AMP contains 5,544 predicted 3D structural models of antimicrobial peptides (AMPs) sourced from the DRAMP database and generated using molecular modeling tools.
• Annotated AMP metadata: Each AMP entry includes source, name, DRAMP ID, and an internal PepID for mapping and retrieval.
• Literature annotations: AMP entries are linked to references from over 10,000 biofilm-related articles.
• Protein–peptide interaction models: Includes in silico molecular docking models, exemplified by docking of 100 AMP structural models against catalytic site residues of sortase C from Corynebacterium striatum.
• Preference scale for candidate selection: A ranking based on docking scores and interacting residues to prioritize AMPs for further investigation.

Scientific Applications:

• Identification of anti-biofilm candidates: Use predicted AMP structures and interaction models to identify AMPs with potential activity against biofilms.
• Prioritization for experimental testing: Docking-based preference scale informs selection of AMPs for in silico, in vitro, and in vivo studies.
• Integration of structural and literature data: Combined structural models and literature annotations support evidence-based selection of AMPs for biofilm inhibition and eradication studies.

Methodology:

3D AMP structures were predicted using molecular modeling techniques from entries sourced in the DRAMP database, and in silico molecular docking analyses were performed to evaluate AMP interactions with biofilm-related targets, including docking of 100 AMP models against the sortase C catalytic site residues of Corynebacterium striatum.