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The ITS2 Database
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A sequence family database built on ECOD structural domains.

Yuxing Liao1, R Dustin Schaeffer1,2, Jimin Pei1,2

  • 1Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Bioinformatics (Oxford, England)
|April 17, 2018
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Summary
This summary is machine-generated.

The ECOD database now includes new protein domain families and improved boundary definitions, enhancing evolutionary classification. These advancements offer valuable resources for understanding protein domain evolution and function.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Evolutionary genomics

Background:

  • The Evolutionary Classification of Domains (ECOD) database classifies protein domains by evolutionary relationships, considering remote and close homology.
  • Existing sequence domain databases like Pfam face challenges when applied to ECOD due to differing domain definition perspectives.

Purpose of the Study:

  • To develop and validate multiple sequence alignments and profiles for ECOD domains.
  • To compare ECOD classifications with existing databases like Pfam and Conserved Domain Database (CDD).

Main Methods:

  • Utilized structural information for building multiple sequence alignments and delineating domain boundaries.
  • Scored structure superposition to validate alignment quality against curated seed alignments in Pfam.
  • Compared ECOD family classifications and domain boundaries with Pfam and CDD.

Main Results:

  • Generated alignments and profiles for ECOD domains, demonstrating quality comparable to Pfam.
  • Identified 27% of ECOD families as new compared to Pfam and 16% compared to CDD.
  • Found that 35% of ECOD family boundaries differ from Pfam and 48% from CDD, with many new families being small due to PDB sampling bias.

Conclusions:

  • The enhanced ECOD database provides new protein domain families and refined boundary classifications.
  • The developed alignments and HMMER profiles are available for download, supporting further research in protein evolution.