XSuLT

XSuLT integrates 3D structural information into multiple-sequence alignments to annotate amino-acid residues and support comparative analyses, comparative modeling, and construct design.

Key Features:

• Residue-level annotations: Provides per-residue annotations including residue depth, chain interactions, ligand interactions, and inter-residue contacts within multiple-sequence alignments.
• Structural and sequence metrics: Evaluates sequence entropy and root mean square deviation (RMSD) to quantify sequence variability and structural divergence.
• Secondary structure and disorder prediction: Incorporates secondary structure prediction and disorder prediction for identification of functional and flexible regions.
• 3D visualization integration: Links formatted alignments to 3D structural representations to map annotations onto structures.
• Alignment optimization: Optimizes multiple-sequence alignments for use in comparative modeling and construct design.
• Export formats: Produces formatted alignment output and annotation data in stand-alone HTML and XML files.

Scientific Applications:

• Comparative protein analysis: Supports comparative analyses of protein evolution to elucidate evolutionary relationships and functional conservation.
• Comparative modeling and construct design: Informs and improves comparative modeling and construct design by providing structure-aware alignment annotations.

Methodology:

Processes submitted multiple-sequence alignments by integrating 3D structural data to enhance residue-level annotations; computes residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, RMSD, and performs secondary structure and disorder prediction, and exports results as formatted HTML and XML.