2dSS

2dSS visualizes and compares protein secondary structure predictions with secondary structure elements derived from 3D structures to identify conserved structural patterns in multiple sequence alignments and assess prediction accuracy.

Key Features:

• 2D-Alignment Functionality: Visualizes conserved secondary structure elements within a multiple sequence alignment (MSA) to highlight structural patterns across homologous proteins.
• Compare Predictions Functionality: Compares outputs from multiple secondary structure prediction tools against secondary structure elements extracted from 3D structures to evaluate prediction accuracy.
• Integration of Predicted and Experimental Data: Integrates outputs from various prediction tools with experimentally determined secondary structure elements from 3D structures for comparative analysis.
• Representation of Secondary Structure Elements: Employs a comprehensive representation approach to display secondary structure elements for clear visualization and comparison.

Scientific Applications:

• Protein Family Analysis: Enables identification of conserved secondary structure motifs within protein families using MSAs.
• Evolutionary Analysis: Supports studies of structural conservation to infer functional or stability-related motifs across species.
• Validation and Improvement of Prediction Methods: Facilitates assessment, validation, and selection of secondary structure prediction algorithms by direct comparison to 3D-derived secondary structures.

Methodology:

Secondary structure elements are extracted from 3D structures, prediction outputs from various secondary structure prediction tools are integrated with these experimental elements, and the combined data are represented on multiple sequence alignments for comparative visualization.