POSA

POSA performs multiple protein structure alignment using a partial order graph representation to accommodate conformational flexibility and compare structural variation.

Key Features:

• Multiple Protein Structure Alignment: Aligns more than two protein structures simultaneously to enable comparative analysis across proteins or protein families.
• Partial Order Graph Representation: Represents protein structures as partial order graphs to capture flexibility and alternative structural paths during alignment.
• User-Defined Anchoring Segments: Incorporates user-specified anchoring segments to guide and constrain alignments toward biologically relevant regions.

Scientific Applications:

• Comparative structural analysis: Enables identification of conserved regions and structural variation across multiple proteins.
• Study of conformational flexibility: Facilitates analysis of flexible regions and alternative conformations within and between proteins.
• Functional inference: Supports investigation of protein function by relating structural motifs and conserved elements to biological activity.
• Evolutionary and family-level comparisons: Aids exploration of evolutionary relationships and structural motifs across species or within protein families.

Methodology:

Protein structures are represented as partial order graphs and aligned using that graph-based representation; user-defined anchoring segments can be incorporated to constrain and guide the alignment.