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A supersecondary structure library and search algorithm for modeling loops in protein structures.

Narcis Fernandez-Fuentes1, Baldomero Oliva, András Fiser

  • 1Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Nucleic Acids Research
|April 18, 2006
PubMed
Summary
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This study introduces a novel fragment-search method for predicting protein loop conformations using a comprehensive database. The approach accurately models protein structures, outperforming existing methods.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Protein loop conformations are crucial for protein function and stability.
  • Accurate prediction of loop structures remains a significant challenge in structural biology.
  • Existing methods often struggle with accuracy and efficiency in predicting loop conformations.

Purpose of the Study:

  • To develop and validate a fragment-search based method for predicting protein loop conformations.
  • To establish a hierarchical, multidimensional database for efficient loop fragment classification.
  • To create a web server for accessible and automated loop conformation prediction.

Main Methods:

  • A hierarchical database of 105,950 loop fragments and flanking secondary structures was constructed.

Related Experiment Videos

  • Candidate fragments were selected based on length, secondary structure, and geometric restraints.
  • Fragment fit was assessed using root mean square deviation (r.m.s.d.) and rigid body clashes.
  • A Z-score combining sequence similarity and dihedral angle propensities was used for final ranking.

    • Main Results:

    • The method achieved high prediction coverage for loops of lengths 4, 8, and 12 (98%, 78%, and 28% respectively) with high accuracy (0.22 Å, 1.38 Å, and 2.47 Å r.m.s.d.).
    • The fragment-search method significantly outperformed a previous database search method by a 5:1 ratio.
    • Confidence cut-offs were established to identify predictions superior to ab initio methods.

    Conclusions:

    • The developed fragment-search method provides an accurate and efficient approach for predicting protein loop conformations.
    • The hierarchical database and Z-score ranking system enhance prediction reliability.
    • The associated web server facilitates broader application in structural biology research.