Protein structures are flexible and undergo structural rearrangements as part of their function. FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure. In FATCAT, the structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0. Dynamic programming is used to find the optimal chaining. The PAIRWISE ALIGNMENT function of the server can be used to align and analyze structures of two protein chains, DATABASE SEARCH function makes it possible to find proteins structurally similar to a given protein, and with HOMOLOGY SEARCH function users can analyze structural differences between a protein and its close homologs.
FATCAT source code is available from github repository
FATCAT 2.0: towards a better understanding of the structural diversity of proteins, Nucleic Acids Research, gkaa443. May 2020