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RepeatsDB: a database of tandem repeat protein structures.

Tomás Di Domenico1, Emilio Potenza, Ian Walsh

  • 1Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy, Department of Biological Chemistry, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina, Department of Information Engineering, University of Padua, 35121 Padova, Italy, Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan, Centre de Recherches de Biochimie Macromoléculaire, CNRS, 34293 Montpellier Cedex 5, France and Institut de Biologie Computationnelle, 34293 Montpellier Cedex 5, France.

Nucleic Acids Research
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PubMed
Summary
This summary is machine-generated.

RepeatsDB is a new database that systematically annotates protein structures containing tandem repeats. This resource aids large-scale analysis of these challenging protein structures.

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Area of Science:

  • Structural Biology
  • Bioinformatics

Background:

  • Tandem repeats in protein structures are difficult to analyze due to degenerate sequences.
  • Previous repeat annotation was fragmented, hindering large-scale studies.

Purpose of the Study:

  • To develop a comprehensive database for systematic annotation of protein tandem repeat structures.
  • To facilitate large-scale analysis and understanding of protein repeat motifs.

Main Methods:

  • Utilized advanced repeat detection algorithms and manual curation.
  • Systematically annotated the entire Protein Data Bank (PDB).
  • Expanded a protein repeat classification schema to include new findings.

Main Results:

  • Identified and annotated 10,745 repeat structures within the PDB.
  • Classified 2,797 structures using an updated classification schema.
  • Provided detailed annotations, including start/end positions, for 321 proteins.

Conclusions:

  • RepeatsDB offers a consistent, high-quality resource for structural protein repeat data.
  • Enables interactive and programmatic access to valuable datasets for researchers.
  • Supports ongoing research and discovery in the field of protein structure analysis.