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Current status of PTMs structural databases: applications, limitations and prospects.

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Summary

This review surveys databases offering 3D structural data for protein post-translational modification (PTM) sites. Understanding PTMs structurally is vital for disease research and protein function analysis.

Keywords:
GlycosylationModified amino acidsPhosphorylationPrediction approachesProtein structuresSecondary structuresStructure/function relationship

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein 3D structures dictate biological functions.
  • Post-translational modifications (PTMs) regulate protein functions by altering physicochemical properties.
  • Aberrant PTMs are linked to human diseases, necessitating structural insights.

Purpose of the Study:

  • To review current databases providing 3D structural data for PTM sites.
  • To highlight the importance of structural PTM data for understanding protein function and disease.
  • To discuss applications and limitations of existing PTM structural databases.

Main Methods:

  • Literature review of PTM databases.
  • Categorization of databases (general vs. specific).
  • Analysis of database applications in silico (PTM site prediction, structure-function relationships).

Main Results:

  • Several PTM databases exist, but few integrate 3D structural data.
  • Databases vary in scope (PTM types, organisms, protein classes).
  • Databases are valuable for machine learning-based PTM site prediction and structure-function analyses.

Conclusions:

  • Databases with 3D PTM structural data are crucial for biological research and disease understanding.
  • Existing databases have limitations, requiring careful data analysis.
  • Further development of integrated, high-quality PTM structural databases is needed.