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

Protein 3D structures, determined by their amino acid sequences, are the support of major crucial biological functions. Post-translational modifications (PTMs) play an essential role in regulating these functions by altering the physicochemical properties of proteins. By virtue of their importance, several PTM databases have been developed and released in decades, but very few of these databases incorporate real 3D structural data. Since PTMs influence the function of the protein and their aberrant states are frequently implicated in human diseases, providing structural insights to understand the influence and dynamics of PTMs is crucial for unraveling the underlying processes. This review is dedicated to the current status of databases providing 3D structural data on PTM sites in proteins. Some of these databases are general, covering multiple types of PTMs in different organisms, while others are specific to one particular type of PTM, class of proteins or organism. The importance of these databases is illustrated with two major types of in silico applications: predicting PTM sites in proteins using machine learning approaches and investigating protein structure-function relationships involving PTMs. Finally, these databases suffer from multiple problems and care must be taken when analyzing the PTMs data.