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The RESID Database of protein structure modifications

J S Garavelli1

  • 1National Biomedical Research Foundation, Protein Information Resource, Washington, DC 20007, USA. garavelli@nbrf.georgetown.edu

Nucleic Acids Research
|December 10, 1998
PubMed
Summary
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The RESID database standardizes protein modification annotations, aiding researchers in understanding covalent binding sites and modified residues. This resource facilitates accurate data curation and analysis in proteomics.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • The PIR-International Protein Sequence Database faced challenges with the increasing volume of post-translational modifications requiring standardized annotation.
  • Accurate annotation of covalent binding sites, modified sites, and cross-links is crucial for understanding protein function.

Purpose of the Study:

  • To construct and release a comprehensive database of protein structure modifications to standardize annotations.
  • To provide a publicly accessible resource for researchers studying protein modifications.

Main Methods:

  • Development of the RESID database starting in 1993.
  • Public release in 1995 as a text database on CD-ROM and via the ATLAS program.
  • Web accessibility established in 1998 on the PIR Web site.

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Main Results:

  • The RESID Database contains systematic and alternate names, Chemical Abstracts Service registry numbers, atomic formulas/weights, enzyme activities, modification indicators (N-terminal, C-terminal, cross-links), keywords, and literature citations.
  • The database supports prediction of peptide atomic masses.
  • Enhancements are underway for graphical molecular structure presentation.

Conclusions:

  • The RESID Database serves as a vital resource for standardized annotation of protein post-translational modifications.
  • It supports diverse applications, including peptide mass prediction and structural visualization.
  • Continued development aims to enhance its utility for the proteomics research community.