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Related Experiment Videos

The protein structure prediction problem could be solved using the current PDB library.

Yang Zhang1, Jeffrey Skolnick

  • 1Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA.

Proceedings of the National Academy of Sciences of the United States of America
|January 18, 2005
PubMed
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The Protein Data Bank (PDB) library aids in constructing full-length protein models. Using the TASSER algorithm, researchers achieved highly accurate models, suggesting the protein-folding problem is solvable with current data.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • The Protein Data Bank (PDB) is a crucial resource for protein structure data.
  • Assessing the PDB's completeness for full-length protein model construction is essential.
  • Unknown protein sequences require reliable methods for structure prediction.

Purpose of the Study:

  • To evaluate the PDB's adequacy for building complete protein models.
  • To assess the accuracy of protein structure prediction using existing PDB templates.
  • To investigate the effectiveness of the TASSER algorithm in de novo protein modeling.

Main Methods:

  • Utilized a benchmark set of 1,489 medium-size proteins.
  • Employed structure alignment to identify homologous templates.

Related Experiment Videos

  • Applied the TASSER algorithm for fragment assembly and force field optimization.

    • Main Results:

    • Found homologous folds with an average RMSD of 2.5 Å and 82% alignment coverage.
    • Generated full-length models with an average RMSD of 2.25 Å, with 97% below 4 Å.
    • Improved aligned regions from 2.5 Å to 1.88 Å, comparable to low-resolution experimental structures.

    Conclusions:

    • The current PDB library is largely sufficient for full-length protein model construction.
    • The TASSER algorithm demonstrates high accuracy in protein structure prediction.
    • Efficient fold recognition algorithms can leverage PDB data to solve the protein-folding problem.