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Multiple protein structure alignment

W R Taylor1, T P Flores, C A Orengo

  • 1Laboratory of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, United Kingdom.

Protein Science : a Publication of the Protein Society
|October 1, 1994
PubMed
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A novel method fuses protein structure comparison and multiple sequence alignment to create a consensus structure. This approach identifies conserved structural cores, improving protein analysis and molecular modeling.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Existing multiple protein structure comparison methods often concatenate pairwise alignments or average coordinates.
  • These approaches may not accurately capture complex structural relationships or identify conserved regions effectively.

Purpose of the Study:

  • To develop an advanced method for comparing and combining multiple protein structures into a consensus.
  • To improve the identification of conserved structural cores and facilitate molecular modeling.

Main Methods:

  • A novel method integrating the SSAP (structure comparison) and MULTAL (multiple sequence alignment) programs.
  • Progressive combination of structures into intermediate consensus structures, evaluated hierarchically.
  • Utilizing interatomic vectors and their coherence (error term) to define conserved regions.

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Main Results:

  • The developed method produces a consensus structure that effectively identifies conserved core regions.
  • Applications demonstrated success in sequence alignment, phylogenetic tree construction, and databank scanning.
  • Visual assessment confirmed the accuracy of the identified structural cores.

Conclusions:

  • The new method offers a robust approach to multiple protein structure comparison and consensus generation.
  • It provides a powerful tool for molecular modeling and understanding protein family relationships.
  • The technique enhances the analysis of structural conservation in proteins.