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Overview of Protein Sorting and Transport

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Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)
12:19

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)

Published on: May 27, 2012

Touring protein space with Matt.

Noah M Daniels1, Anoop Kumar, Lenore J Cowen

  • 1Tufts University, Medford.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|April 6, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new protein structure clustering method using the Matt program. The method approximately matches the SCOP database at the superfamily level, offering insights into protein fold organization.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Hierarchical clustering schemes are crucial for organizing protein structural domains.
  • Previous methods like Dali/FSSP largely replicated curated schemes (e.g., SCOP) at the family level.
  • It remained unclear if purely geometric methods could approximate SCOP at superfamily and fold levels.

Purpose of the Study:

  • To develop a hierarchical clustering scheme for protein structural domains based on geometric dissimilarity using the Matt program.
  • To assess the ability of geometric, distance-based measures to approximate the SCOP database at superfamily and fold levels.
  • To compare the performance of the Matt program with DaliLite for protein structure alignment.

Main Methods:

  • Utilized the Matt structure alignment program for protein space analysis.
  • Developed a hierarchical clustering scheme based on geometric dissimilarity.
  • Compared the clustering results with the SCOP database and evaluated Matt and DaliLite performance.

Main Results:

  • The Matt-based clustering scheme approximately matches SCOP at the superfamily level.
  • Qualitative differences in performance were observed between Matt and DaliLite.
  • A new benchmark set, Mattbench, was created for testing sequence aligners on distantly homologous proteins.

Conclusions:

  • Purely structural, geometric clustering can approximate established protein classification schemes (SCOP) at superfamily levels.
  • The study contributes to the understanding of protein fold space organization.
  • The Mattbench dataset provides a valuable resource for evaluating protein sequence alignment tools.