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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

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.

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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.

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.

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