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mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

Runze Dong1, Shuo Pan1, Zhenling Peng2

  • 1School of Mathematical Sciences, Nankai University, Tianjin 300071, China.

Nucleic Acids Research
|May 23, 2018
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Summary
This summary is machine-generated.

The mTM-align server offers efficient protein structure comparison through fast database searching and accurate multiple structure alignment. This tool significantly outperforms existing methods in both speed and precision for analyzing protein structural data.

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Area of Science:

  • Structural bioinformatics
  • Computational biology

Background:

  • The Protein Data Bank (PDB) has seen a rapid increase in protein structures.
  • Efficient algorithms for protein structure comparison are urgently needed.

Purpose of the Study:

  • To present the mTM-align server for efficient protein structure database searching and multiple structure alignment.
  • To introduce novel algorithms that enhance speed and accuracy in protein structure analysis.

Main Methods:

  • Development of a heuristic algorithm and hierarchical organization for accelerated database searching.
  • Implementation of the mTM-align algorithm for precise multiple structure alignment.
  • Integration of database search and multiple structure alignment functionalities.

Main Results:

  • The mTM-align server demonstrates superior performance compared to peer methods in speed and accuracy.
  • Database search for a medium-sized structure (∼300 residues) takes 2-5 minutes.
  • Multiple structure alignment for approximately 10 medium-sized structures takes only a few seconds.

Conclusions:

  • The mTM-align server provides a powerful and efficient solution for protein structure comparison.
  • The unique interplay between database search and alignment offers comprehensive structural analysis capabilities.
  • The server is freely available for researchers, facilitating advancements in structural bioinformatics.