PALSSE

PALSSE: Predictive assignment of protein secondary structure elements

PALSSE predicts and assigns residues in protein structures to linear secondary structure elements (SSEs) using Cα coordinates, enabling overlapping consecutive elements and allowing residues to be assigned multiple secondary structure types.

Key Features:

• Linear SSE Assignment: Attributes residues to linear SSEs rather than single-residue states, permitting overlap of consecutive elements and multiple structural assignments per residue.
• High Coverage Prediction: Assigns approximately 80% of residues in a protein chain to SSEs, exceeding coverage reported for DSSP (53%) and P-SEA (57%).
• Robustness to Coordinate Errors: Maintains performance in the presence of coordinate errors and defines SSEs in poorly refined or low-resolution structures.
• Consistency with Established Methods: Produces secondary structure delineations consistent with human judgment and established methods such as DSSP.

Scientific Applications:

• Vector-Based Protein Similarity Searches: Improves precision of vector-based structural comparisons through detailed SSE assignments.
• Structural Analysis: Supports representation and computational analysis of protein structures based on secondary structure patterns.

Methodology:

PALSSE analyzes protein Cα atomic coordinates to predictively assign residues to linear secondary structure elements, allowing overlapping elements to capture residues participating in multiple structural motifs and enabling reliable SSE definition in low-resolution or error-prone structural datasets.