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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Protein Organization

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The primary structure of a protein is its amino acid sequence.
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Peptide Identification Using Tandem Mass Spectrometry

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MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models,

Shintaro Minami1, Kengo Sawada, George Chikenji

  • 1Department of Computational Science and Engineering, Nagoya University, Nagoya 464-8603, Japan.

BMC Bioinformatics
|January 22, 2013
PubMed
Summary

We developed MICAN, a novel protein structure alignment algorithm, to identify structural relationships. MICAN is the fastest and most accurate tool for non-sequential alignments, aiding evolutionary and biophysical studies.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure comparison is crucial for understanding protein evolution and physical chemistry.
  • Identifying proteins with similar secondary structure packing but different topologies requires accurate, sequence-order-independent methods.

Purpose of the Study:

  • To develop a novel protein structure alignment algorithm for identifying structural relationships, particularly non-sequential ones.
  • To create a tool that can handle complex protein structures including multiple chains and inverse secondary structures.

Main Methods:

  • Developed MICAN (Multiple-chain, Inverse direction, Cα only, Alternative, Non-sequential alignment) algorithm.
  • Utilized multiple vector representation for secondary structure elements (SSEs) to handle bent or twisted SSEs.
  • Compared MICAN against nine other alignment programs using various benchmark datasets and evaluation methods.

Main Results:

  • MICAN demonstrated superior performance in reproducing reference alignments for non-sequential protein structures.
  • The algorithm achieved top-level performance on sequential structure alignment tasks, despite not being specialized for them.
  • MICAN was identified as the fastest non-sequential structure alignment program among those evaluated.

Conclusions:

  • MICAN is a highly accurate and efficient tool for detecting non-trivial protein structural relationships, including circular permutations and segment-swapping.
  • The algorithm facilitates the automated identification of complex protein structural similarities previously requiring manual expert analysis.
  • MICAN's source code is publicly available for download, promoting further research and application.