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PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional

Fuyi Li1,2, Cunshuo Fan3, Tatiana T Marquez-Lago4

  • 1Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.

Briefings in Bioinformatics
|June 5, 2019
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Summary

PRISMOID is a new database providing 3D structural information for post-translational modifications (PTMs). This resource addresses the lack of 3D structural data for PTMs, aiding research into their functional and mechanical roles.

Keywords:
Bioinformaticsdatabasefunctional impactmutationpost-translational modifications

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Post-translational modifications (PTMs) are crucial for cell signaling and biological processes.
  • Existing databases primarily focus on protein sequences, neglecting the 3D structural context of PTMs.
  • This data deficiency limits studies on PTM 3D structural signatures.

Purpose of the Study:

  • To introduce PRISMOID, a novel, free, and publicly accessible 3D structure database for post-translational modifications (PTMs).
  • To provide an interactive knowledge base focusing on the 3D structural context of PTM sites, including mutations and their functional impacts.
  • To facilitate research on the sequence-structural-functional relationships of PTMs and mutation-PTM site interactions.

Main Methods:

  • Development of PRISMOID, a database integrating 17,145 PTM sites across 3,919 protein 3D structures, covering 37 PTM types.
  • Comprehensive annotation of PTM sites on 3D structures, including mutation data, secondary structure, solvent accessibility, domain context, disordered regions, and sequence alignments.
  • Implementation of interactive search functions, data browsing, and visualization tools using JavaScript packages.

Main Results:

  • PRISMOID version 1 contains extensive data on PTMs, their structural context, and associated mutations.
  • The database offers detailed annotations and visualization of PTM sites within protein structures.
  • Interactive search and download functionalities are available for user convenience.

Conclusions:

  • PRISMOID serves as an invaluable resource for biologists and bioinformaticians studying PTMs.
  • The database aids in understanding the sequence-structural-functional relationships of PTMs and mutation impacts.
  • PRISMOID promotes discovery in PTM research by providing crucial 3D structural insights.