ArticleDatabase : the journal of biological databases and curation2014
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- StrucPTM: a database of structurally validated protein modifications and their conformational variation.Bioinformatics (Oxford, England) · 2026Article
- Integrative Analysis of Post-Translational Modifications Identifies a PTM-Enriched Regulatory Core in Human Metabolic Enzymes.Metabolites · 2026Article
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- Artificial Intelligence Transforming Post-Translational Modification Research.Bioengineering (Basel, Switzerland) · 2024Review
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network.bioRxiv : the preprint server for biology · 2024Article
- Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
- AQcalc: A web server that identifies weak molecular interactions in protein structures.Protein science : a publication of the Protein Society · 2023Article
- Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.Magnetic resonance (Gottingen, Germany) · 2023Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- An atlas of posttranslational modifications on RNA binding proteins.Nucleic acids research · 2022Article
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology.Antibody therapeutics · 2022Review
- PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.Briefings in bioinformatics · 2020Article
- Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB).International journal of molecular sciences · 2020Article
- Defining the genetic control of human blood plasma N-glycome using genome-wide association study.Human molecular genetics · 2019Article
- Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools.International journal of molecular sciences · 2018Review
- SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure.Molecules (Basel, Switzerland) · 2018Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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