iSARST

iSARST performs high-throughput protein structural similarity searches to identify co-linear and circularly permuted homologs and support protein function annotation.

Key Features:

• SARST and CPSARST search methods: Uses SARST to identify common structural homologs and CPSARST to detect homologs with circular permutations.
• Batch processing: Supports batch-processing of large datasets from multiple queries.
• Input formats: Accepts multiple Protein Data Bank (PDB) or Structural Classification of Proteins (SCOP) entry IDs or an archive file containing numerous structures.
• Hit refinement: Refines ordering of hits using structure alignment tools FAST, TM-align, and SAMO.
• Compute infrastructure: Executes refinement steps on a PC cluster for increased speed and precision.
• Output types: Produces detailed tables listing co-linear and circularly permuted homologs and provides a functional summary of best hits.
• Detection capability: Capable of handling both co-linear homologs and circularly permuted homologs in batch comparisons.

Scientific Applications:

• Protein function annotation: Supports annotation of functionally unknown or hypothetical proteins by identifying structurally similar proteins.
• Large-scale structural screening: Enables scanning of structural databases for homolog detection across many queries.
• Evolutionary and structural analysis: Facilitates identification of circular permutations for studies of protein evolution and structural variation.

Methodology:

Searches use SARST and CPSARST to scan target structural databases, with hit ordering refined by FAST, TM-align, and SAMO; computations are executed on a PC cluster.