AS2TS

AS2TS performs protein structure comparison and homology-based modeling to analyze amino acid sequences and produce PDB-format 3D models using LGA, PSI-BLAST, and AL2TS.

Key Features:

• LGA method: LGA enables sequence-dependent and sequence-independent comparison of protein structures and structural fragments.
• Scoring and Classification: LGA-generated data are used in scoring functions that rank structural similarity and support classification of proteins by structural features.
• Clustering of Protein Fragments: Clustering of similar structural fragments identifies conserved motifs and domains across proteins.
• AL2TS (sequence-structure alignment translation): AL2TS converts sequence–structure alignment data into standard PDB atom records for homology-based model building.
• PSI-BLAST PDB Analysis: PSI-BLAST searches against the PDB to identify closest structural counterparts for given amino acid sequences.
• Automated 3D Model Generation: The system automatically creates draft 3D models from identified structural templates.
• Sequence Alignment: Amino acid sequences are aligned to identify regions of similarity for downstream comparison and modeling.

Scientific Applications:

• Protein Structure Comparison: Compare protein structures to identify evolutionary relationships or functional similarities.
• Structure-Based Drug Design: Provide 3D target conformations to inform structure-based drug design.
• Functional Annotation: Predict functions of uncharacterized proteins by comparison with known structures.
• Protein Engineering: Support rational design of proteins with desired properties through structural analysis.

Methodology:

Sequence alignment to identify regions of similarity, LGA-based local and global structure comparison, and automated generation of 3D models from identified templates.