SeSAW

SeSAW identifies functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities and quantifying conservation at the residue level.

Key Features:

• Sequence and structural analysis: Integrates sequence alignment and structural comparison to detect conserved motifs across proteins.
• Residue-level quantification: Quantifies similarities at the level of individual residues to pinpoint conserved regions.
• Annotated alignments and superpositions: Produces annotated 2D alignments and 3D structural superpositions to relate sequence and structural similarity.
• Support for diverse models: Accepts experimentally determined query structures and homology models for comparative analysis.

Scientific Applications:

• Functional inference: Identifies conserved motifs to support annotation and prediction of protein function.
• Evolutionary analysis: Reveals sequence-structure conservation patterns useful for studying evolutionary relationships.
• Disease mechanism investigation: Highlights conserved regions that may underlie the molecular basis of diseases.
• Protein engineering and drug design: Informs design efforts by locating functionally important conserved residues and structural motifs.

Methodology:

Performs systematic comparisons of query proteins against a database of known structures, locates sequence and structural similarities, and quantifies those similarities at the residue level considering both sequence homology and structural conformation.