Hammock

Hammock clusters short peptide sequences by shared sequence motifs to identify specificity determinants relevant to protein–protein interactions and short linear motifs in disordered protein regions.

Key Features:

• Large-Scale Clustering: Identifies clusters of short peptide sequences with shared specificity motifs from large datasets.
• Rapid Clustering: Performs rapid identification of sequence clusters that carry shared motifs.
• Multiple Sequence Alignment: Generates multiple sequence alignments for identified clusters.
• Detection of Motif Variants: Reveals secondary clusters that accommodate sequence deviations and motif variants.
• Versatility in Data Sources: Processes peptide datasets originating from diverse experimental sources.
• Scalability: Scales to datasets ranging from small collections to datasets an order of magnitude larger.

Scientific Applications:

• Short Linear Motif Analysis: Analyzes protein–protein interactions mediated by short linear motifs in disordered regions by clustering motif-containing peptides.
• SH3 Domain Ligand Identification: Identifies and characterizes ligands for SH3 domains from peptide datasets.
• Monoclonal Antibody Epitope Mapping: Identifies clusters that mimic monoclonal antibody epitopes and reveals variant epitope clusters.
• Interaction Specificity and Dynamics: Explores interaction specificity and dynamics by grouping peptides that share binding motifs.

Methodology:

Hammock rapidly identifies sequence clusters that share motifs and generates multiple sequence alignments for those clusters.