SANA

SANA performs protein structure alignment to identify core structural correspondences and conserved functional sites while accommodating internal repeats, insertions/deletions (indels), and circular permutations.

Key Features:

• Core Region Alignment: Aligns core regions by identifying connected components within a network of neighboring, geometrically compatible aligned fragment pairs (AFPs).
• Multi-Objective Optimization Refinement: Refines initial alignments using multi-objective optimization to improve alignment accuracy and biological relevance.
• Sequential and Non-Sequential Alignments: Produces both sequential and non-sequential alignments to accommodate structural rearrangements such as circular permutations.
• Handling Structural Variations: Handles internal repeats and insertions/deletions (indels) to align complex structural regions accurately.
• Identification of Functional Sites: Reveals conserved functional sites within alignments to inform functional and evolutionary interpretation.
• Benchmarking and Ranking Criterion: Performance evaluated against DALI, CE, and MATT on benchmark datasets and includes a fold-similarity ranking criterion comparable or superior to the Z-score of CE in most cases.

Scientific Applications:

• Comparative Structural Analysis: Compares protein structures across species or within families to facilitate evolutionary and structural relationship studies.
• Functional Annotation: Identifies conserved functional sites to support prediction of function for uncharacterized proteins based on structural similarity.
• Drug Discovery and Design: Maps conserved functional sites and structural correspondences to inform drug target identification and rational design.

Methodology:

Constructs a network of geometrically compatible aligned fragment pairs (AFPs) to identify connected components as core alignments, then refines alignments via multi-objective optimization.