VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9000, Belgium.
Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, Ghent 9000, Belgium.
J Proteome Res. 2020 Aug 7;19(8):3478-3486. doi: 10.1021/acs.jproteome.0c00306. Epub 2020 Jun 18.
Protein phosphorylation is a key post-translational modification in many biological processes and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation, and functional analysis of phosphosites are therefore crucial to understand their various roles. Phosphosites are mainly analyzed through phosphoproteomics, which has led to increasing amounts of publicly available phosphoproteomics data. Several resources have been built around the resulting phosphosite information, but these are usually restricted to the protein sequence and basic site metadata. What is often missing from these resources, however, is context, including protein structure mapping, experimental provenance information, and biophysical predictions. We therefore developed Scop3P: a comprehensive database of human phosphosites within their full context. Scop3P integrates sequences (UniProtKB/Swiss-Prot), structures (PDB), and uniformly reprocessed phosphoproteomics data (PRIDE) to annotate all known human phosphosites. Furthermore, these sites are put into biophysical context by annotating each phosphoprotein with per-residue structural propensity, solvent accessibility, disordered probability, and early folding information. Scop3P, available at https://iomics.ugent.be/scop3p, presents a unique resource for visualization and analysis of phosphosites and for understanding of phosphosite structure-function relationships.
蛋白质磷酸化是许多生物过程中的关键翻译后修饰，与癌症和代谢紊乱等人类疾病有关。因此，准确识别、注释和功能分析磷酸化位点对于理解它们的各种作用至关重要。磷酸化位点主要通过磷酸蛋白质组学进行分析，这导致了越来越多的公开可用的磷酸蛋白质组学数据。已经围绕产生的磷酸化位点信息构建了几个资源，但这些资源通常仅限于蛋白质序列和基本位点元数据。然而，这些资源通常缺少上下文信息，包括蛋白质结构映射、实验来源信息和物理预测。因此，我们开发了 Scop3P：一个全面的人类磷酸化位点数据库，包含其完整的上下文信息。Scop3P 集成了序列（UniProtKB/Swiss-Prot）、结构（PDB）和统一重新处理的磷酸蛋白质组学数据（PRIDE），以注释所有已知的人类磷酸化位点。此外，通过为每个磷酸化蛋白注释每个残基的结构倾向、溶剂可及性、无序概率和早期折叠信息，将这些位点置于物理化学环境中。Scop3P 可在 https://iomics.ugent.be/scop3p 上获得，是可视化和分析磷酸化位点以及理解磷酸化位点结构-功能关系的独特资源。
