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Related Concept Videos

Protein Folding01:22

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Protein Folding01:25

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Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay
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Published on: October 20, 2018

ModLink+: improving fold recognition by using protein-protein interactions.

Oriol Fornes1, Ramon Aragues, Jordi Espadaler

  • 1Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Catalonia, Spain. boliva@imim.es

Bioinformatics (Oxford, England)
|April 10, 2009
PubMed
Summary
This summary is machine-generated.

The improved ModLink+ method enhances protein fold prediction accuracy by incorporating protein-protein interactions, significantly increasing the number of proteins with assigned folds compared to existing tools.

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09:18

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Published on: May 30, 2017

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein fold prediction is crucial for understanding protein function.
  • Sequence alignment methods are common but have limitations in accuracy and coverage.
  • Protein-protein interactions can improve fold assignment accuracy.

Purpose of the Study:

  • To present an improved protein fold assignment method, ModLink+.
  • To address the limitation of low coverage in previous methods.
  • To compare ModLink+ with state-of-the-art fold assignment techniques.

Main Methods:

  • Utilized protein sequences with known structures from the Structural Classification Of Proteins (SCOP).
  • Incorporated known protein-protein interactions from the Database of Interacting Proteins (DIP).
  • Developed and tested the improved ModLink+ algorithm.

Main Results:

  • ModLink+ achieved a positive predictive value (PPV) of >90% for fold assignment at an e-value cutoff of 10(-3), outperforming PSI-BLAST (75%), HHSearch (83%), and PRC (81%).
  • ModLink+ increased fold assignment coverage to 30-45% of proteins, compared to <25% with the previous method.
  • In the yeast proteome, ModLink+ combined with PSI-BLAST assigned folds to 3738 proteins, significantly more than PSI-BLAST alone (2122), HHSearch (2969), or PRC (2826).

Conclusions:

  • ModLink+ significantly improves the accuracy and coverage of protein fold prediction.
  • The integration of protein-protein interactions is key to the enhanced performance.
  • ModLink+ offers a powerful tool for structural bioinformatics and protein function prediction.