SeqCP

SeqCP identifies circularly permuted proteins (CPMs) from protein sequences to enable sequence-based detection and annotation of CPMs in proteins without known structures.

Key Features:

• Sequence-based detection: Detects circularly permuted proteins using sequence information without reliance on structural data.
• Alignment strategies: Analyzes both normal and duplicated sequence alignments to reveal permutation signals.
• Candidate CP site identification: Identifies candidate circular permutation sites within sequence alignments.
• CPM pair establishment: Establishes connections between protein sequences as CPM pairs.
• Training data: Trained using data from the Circular Permutation Database.
• Validation and performance: Validated on nonredundant datasets from the Protein Data Bank with an area under curve (AUC) of 0.9.

Scientific Applications:

• Annotation of hypothetical proteins: Enables annotation of proteins lacking known structures by identifying potential CPM relationships.
• Discovery of CPM pairs: Facilitates discovery of previously unidentified circularly permuted protein pairs.
• Functional annotation: Supports functional inference for proteins through detected permutation-based relationships.
• Structural biology and protein engineering: Provides sequence-based evidence of permutation that can inform structural studies and engineering strategies.

Methodology:

Analyzes normal and duplicated sequence alignments to identify candidate CP sites and establish CPM connections; trained on the Circular Permutation Database and validated using nonredundant Protein Data Bank datasets (AUC 0.9).