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Related Experiment Video

Updated: May 22, 2026

A Postoperative Evaluation Guideline for Computer-Assisted Reconstruction of the Mandible
10:42

A Postoperative Evaluation Guideline for Computer-Assisted Reconstruction of the Mandible

Published on: January 28, 2020

[Verification of the PREFAB alignment database].

T V Astakhova, M N Lobanov, I V Poverennaia

    Biofizika
    |May 19, 2012
    PubMed
    Summary
    This summary is machine-generated.

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    Researchers verified the PREFAB database, finding discrepancies with Protein Data Bank (PDB) sequences. After cleaning and refining, a new golden standard protein alignment database, PREFAB-P, was created with 581 high-quality alignments.

    Area of Science:

    • Bioinformatics
    • Structural Biology
    • Computational Biology

    Context:

    • The PREFAB database serves as a benchmark for evaluating protein sequence alignment methods.
    • Discrepancies between existing databases can impact the reliability of computational biology tools.
    • Accurate protein alignments are crucial for understanding protein function and evolution.

    Purpose:

    • To verify the integrity of the PREFAB database as a golden standard for protein alignments.
    • To identify and rectify sequence and alignment errors within the PREFAB database by cross-referencing with the Protein Data Bank (PDB).
    • To establish a refined, high-quality protein alignment database for downstream applications.

    Summary:

    • Verification of the PREFAB database revealed significant sequence differences compared to the PDB database.

    Related Experiment Videos

    Last Updated: May 22, 2026

    A Postoperative Evaluation Guideline for Computer-Assisted Reconstruction of the Mandible
    10:42

    A Postoperative Evaluation Guideline for Computer-Assisted Reconstruction of the Mandible

    Published on: January 28, 2020

  • Over 1000 alignments were excluded or edited due to gaps, substitutions, or insertions relative to PDB sequences.
  • SCOP domain analysis confirmed shared family membership for only 502 alignments.
  • A new golden standard database, PREFAB-P, was constructed from the curated PREFAB data, containing 581 unique and validated alignments.

    • Impact:

    • The creation of PREFAB-P provides a more reliable resource for benchmarking protein alignment algorithms.
    • Improved accuracy in protein alignments can lead to better predictions of protein function and structure.
    • This work highlights the importance of rigorous database curation in bioinformatics research.