FATCAT: a web server for flexible structure comparison and structure similarity searching

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• Protein structure comparison is crucial for understanding biological function and evolution.
• Existing web resources rely on rigid alignment algorithms, limiting their ability to detect subtle structural differences.
• Flexible alignment is needed to accurately compare protein structures with internal rearrangements.

Purpose of the Study:

• To introduce the FATCAT server, a novel web-based tool for flexible protein structure comparison.
• To provide access to two algorithms: FATCAT-pairwise for comparing two structures and FATCAT-search for database searching.
• To enable the identification of hinges and internal rearrangements in protein structures.

Main Methods:

• The FATCAT server implements a flexible protein structure comparison algorithm.
• FATCAT-pairwise performs pairwise flexible structure comparison, reporting alignment and statistical significance (P-value).
• FATCAT-search enables database searching for structurally similar proteins using a query structure.

Main Results:

• The FATCAT server provides accurate structural alignments by accounting for internal rearrangements.
• Users can visualize superimposed structures online or download them in PDB format.
• FATCAT-search returns a ranked list of similar protein structures based on P-values.

Conclusions:

• The FATCAT server offers a significant advancement over rigid alignment methods for protein structure comparison.
• It facilitates the identification of conformational changes and structural similarities, aiding biological research.
• The server is a valuable resource for structural biologists and bioinformaticians.