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PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.

Pierrick Craveur1, Joseph Rebehmed2, Alexandre G de Brevern3

  • 1INSERM, U 1134, DSIMB, F-75739 Paris, France, Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d'Excellence GR-Ex, F-75739 Paris, FranceINSERM, U 1134, DSIMB, F-75739 Paris, France, Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d'Excellence GR-Ex, F-75739 Paris, FranceINSERM, U 1134, DSIMB, F-75739 Paris, France, Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d'Excellence GR-Ex, F-75739 Paris, FranceINSERM, U 1134, DSIMB, F-75739 Paris, France, Univ Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d'Excellence GR-Ex, F-75739 Paris, France pierrick.craveur@inserm.fr.

Database : the Journal of Biological Databases and Curation
|May 27, 2014
PubMed
Summary

The Posttranslational Modification Structural Database (PTM-SD) offers crucial 3D structural insights into protein modifications. This resource aids in understanding sequence-structure-function relationships and PTM prediction.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Proteomics

Background:

  • Posttranslational modifications (PTMs) are vital chemical alterations to proteins, influencing biological functions.
  • Existing PTM databases lack comprehensive 3D structural data for these modifications.
  • Understanding PTMs in 3D is essential for deciphering protein function and regulation.

Purpose of the Study:

  • To introduce the Posttranslational Modification Structural Database (PTM-SD).
  • To provide a valuable 3D structural resource for experimentally verified PTMs.
  • To facilitate research on sequence-structure-function relationships influenced by PTMs.

Main Methods:

  • Integrated PTM data from multiple sources, including Protein DataBank (PDB), dbPTM, and PTMCuration.
  • Developed accurate PTM detection within structural data.
  • Enabled browsing and advanced querying by PDB ID, UniProt accession, PTM type, and structural features.

Main Results:

  • PTM-SD offers detailed information on structurally solved modified residues.
  • The database provides insights into local protein conformation, secondary structure, and Protein Blocks.
  • Enables statistical analysis of PTM datasets.

Conclusions:

  • PTM-SD is a unique resource for exploring PTMs in the context of protein 3D structures.
  • The database supports comparative modeling and PTM prediction protocols.
  • Facilitates deeper understanding of PTMs in biological systems.