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

Pierrick Craveur, Joseph Rebehmed, Alexandre G de Brevern

Journal: Database : the journal of biological databases and curation 2014;2014():bau041

PMID: 24857970

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Abstract

Posttranslational modifications (PTMs) define covalent and chemical modifications of protein residues. They play important roles in modulating various biological functions. Current PTM databases contain important sequence annotations but do not provide informative 3D structural resource about these modifications. Posttranslational modification structural database (PTM-SD) provides access to structurally solved modified residues, which are experimentally annotated as PTMs. It combines different PTM information and annotation gathered from other databases, e.g. Protein DataBank for the protein structures and dbPTM and PTMCuration for fine sequence annotation. PTM-SD gives an accurate detection of PTMs in structural data. PTM-SD can be browsed by PDB id, UniProt accession number, organism and classic PTM annotation. Advanced queries can also be performed, i.e. detailed PTM annotations, amino acid type, secondary structure, SCOP class classification, PDB chain length and number of PTMs by chain. Statistics and analyses can be computed on a selected dataset of PTMs. Each PTM entry is detailed in a dedicated page with information on the protein sequence, local conformation with secondary structure and Protein Blocks. PTM-SD gives valuable information on observed PTMs in protein 3D structure, which is of great interest for studying sequence-structure- function relationships at the light of PTMs, and could provide insights for comparative modeling and PTM predictions protocols. Database URL: PTM-SD can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/PTM-SD/.

Address: INSERM, 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 [email protected].; INSERM, 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.; INSERM, 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 [email protected].

DOI: 10.1093/database/bau041

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MeSH Terms: Databases, Protein, Molecular Sequence Annotation, Protein Processing, Post-Translational, Proteins