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Related Experiment Videos

PISCES: recent improvements to a PDB sequence culling server.

Guoli Wang1, Roland L Dunbrack

  • 1Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary
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The PISCES server refines the Protein Data Bank (PDB) by providing high-resolution structures based on sequence identity and quality. It offers improved sequence identity accuracy and new culling options for researchers.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) is a crucial resource for structural biology.
  • Efficiently culling the PDB based on sequence identity and structural quality is essential for data analysis.
  • Existing methods for sequence identity determination may have limitations in accuracy and completeness.

Purpose of the Study:

  • To introduce the enhanced PISCES database server for culling the PDB.
  • To provide researchers with accurate sequence identity information and improved structural data filtering.
  • To offer flexible culling options, including entry-level and chain-level filtering.

Main Methods:

  • Utilizes a combination of PSI-BLAST and structure-based alignments for sequence identity determination.

Related Experiment Videos

  • Implements both chain-specific and entry-specific culling criteria.
  • Integrates with the RCSB PDB search functionality for seamless data input.

    • Main Results:

    • PISCES provides more accurate sequence identities through structure-based alignments compared to PSI-BLAST alone.
    • The server enables culling by-entry, ensuring unique structural entries in the output list.
    • Fully annotated sequences, including gene name and species, are provided.
    • Weekly data updates ensure access to the latest PDB information.

    Conclusions:

    • The re-engineered PISCES server offers a powerful and flexible tool for researchers working with PDB data.
    • Improved accuracy in sequence identity determination and new culling functionalities enhance data analysis capabilities.
    • PISCES facilitates the selection of high-resolution structures meeting specific sequence and quality criteria.