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Introduction

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.

TOPS++FATCAT Similarity Search

This server performs the TOPS++FATCAT similarity search for a given protein structure against a database and provides the top hits of similar structures.
Try the TOPS++FATCAT Similarity Database Search Server.

Benchmark Analysis Results

  • Rigid TOPS++FATCAT and FATCAT results.

  • Flexible TOPS++FATCAT and FATCAT results.



    TOPS++FATCAT Reference: Mallika Veeramalai, Yuzhen Ye and Adam Godzik. "TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model" BMC Bioinformatics ,9:358, 2008.

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    This research was supported by NIH grant P20 GM076221 JCMM (Joint Center for Molecular Modeling)

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