A common mechanism for protein regulation is through post-translational modifications(PTMs), which can affect the activity, subcellular localization, and stability of proteins. Most of the available databases on protein PTMs collect and integrate PTM information from different resources, but they provide very little or no information on the reliability of the identified PTM sites, experimental condition, pathological status and their functional relevance. In order to remove the hidden layer on the proteomics experiments using different versions of sequence databases with different search settings and FDR controls, and to potentially look for additional modifications that could explain the identified spectra from the original experiments, we created Scop3PTM.

Scop3PTM is an interactive knowledge-base on human PTMs built by reprocessing all available human proteomics experiments from PRIDE with the uniform and updated sequence database, search settings and FDR control. Scop3PTM knowledgebase contains 120 different biological modifications (phosphorylation, acetylation etc) and more than 300 non-biological modifications (artefacts and chemical derivatives).

Furthermore, PTM sites are put into sequence, structural and biophysical context by annotating every human protein with per-residue structural propensity, solvent accessibility, disordered probability, backbone and sidechain dynamics, and early folding information. Scop3PTM acts as a much-needed bridge between the fields of proteomics, structural bioinformatics and intrinsically disordered proteins (IDPs), and presents a unique resource for visualization, and to understand the impact of PTM-sites on structure-function relationship of proteins.

A common mechanism for protein regulation is through post-translational modifications(PTMs), which can affect the activity, subcellular localization, and stability of proteins. Most of the available databases on protein PTMs collect and integrate PTM information from different resources, but they provide very little or no information on the reliability of the identified PTM sites, experimental condition, pathological status and their functional relevance. In order to remove the hidden layer on the proteomics experiments using different versions of sequence databases with different search settings and FDR controls, and to potentially look for additional modifications that could explain the identified spectra from the original experiments, we created Scop3PTM. Scop3PTM is an interactive knowledge-base on human PTMs built by reprocessing all available human proteomics experiments from PRIDE with the uniform and updated sequence database, search settings and FDR control. Scop3PTM knowledgebase contains 120 different biological modifications (phosphorylation, acetylation etc) and more than 300 non-biological modifications (artefacts and chemical derivatives). Furthermore, PTM sites are put into sequence, structural and biophysical context by annotating every human protein with per-residue structural propensity, solvent accessibility, disordered probability, backbone and sidechain dynamics, and early folding information. Scop3PTM acts as a much-needed bridge between the fields of proteomics, structural bioinformatics and intrinsically disordered proteins (IDPs), and presents a unique resource for visualization, and to understand the impact of PTM-sites on structure-function relationship of proteins.