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Protein structure analysis and comparison are major challenges in structural bioinformatics.
Despite the existence of many tools and algorithms, very few of them have managed to
capture the intuitive understanding of protein structures developed in
structural biology, especially in the context of rapid database searches.
Such intuitions could help speed up similarity searches and make it easier
to understand the results of such analyses.
TOPS++FATCAT algorithm uses an intuitive description of the proteins structures
as captured in the popular TOPS diagrams to limit the search space of the aligned
fragment pairs (AFPs) in the flexible alignment of protein structures
performed by the FATCAT algorithm. Many of the AFPs considered in the
FATCAT alignment could be easily eliminated from the comparison by
constraining the alignment region. Here we explore constraints obtained
from the TOPS+ strings alignment, which identifies topologically equivalent
secondary structure elements (alpha helices, beta strands, and loops) for this
purpose. Such equivalences define blocks that restrict the alignment region;
AFPs that fall outside these regions are simply not considered.
Mallika Veeramalai, Yuzhen Ye and Adam Godzik.
"TOPS++FATCAT: fast flexible structural alignment using constraints derived
from TOPS+ Strings Model"