
Scop3P : a comprehensive resource of human phosphosites within their full context
- Author
- Pathmanaban Ramasamy (UGent) , Demet Turan (UGent) , Natalia Tichshenko (UGent) , Niels Hulstaert (UGent) , Elien Vandermarliere (UGent) , Wim Vranken and Lennart Martens (UGent)
- Organization
- Abstract
- 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.
- Keywords
- Biochemistry, General Chemistry, phosphorylation, PTM, protein structure, proteomics, reprocessing, PHOSPHORYLATION SITES, POSTTRANSLATIONAL MODIFICATIONS, PROTEIN-PHOSPHORYLATION, PROTEOMICS DATA, PREDICTION, SEQUENCE, (MSPIP)-P-2, MECHANISM, SPECIFICITY, UNIVERSAL
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8671252
- MLA
- Ramasamy, Pathmanaban, et al. “Scop3P : A Comprehensive Resource of Human Phosphosites within Their Full Context.” JOURNAL OF PROTEOME RESEARCH, vol. 19, no. 8, 2020, pp. 3478–86, doi:10.1021/acs.jproteome.0c00306.
- APA
- Ramasamy, P., Turan, D., Tichshenko, N., Hulstaert, N., Vandermarliere, E., Vranken, W., & Martens, L. (2020). Scop3P : a comprehensive resource of human phosphosites within their full context. JOURNAL OF PROTEOME RESEARCH, 19(8), 3478–3486. https://doi.org/10.1021/acs.jproteome.0c00306
- Chicago author-date
- Ramasamy, Pathmanaban, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, and Lennart Martens. 2020. “Scop3P : A Comprehensive Resource of Human Phosphosites within Their Full Context.” JOURNAL OF PROTEOME RESEARCH 19 (8): 3478–86. https://doi.org/10.1021/acs.jproteome.0c00306.
- Chicago author-date (all authors)
- Ramasamy, Pathmanaban, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, and Lennart Martens. 2020. “Scop3P : A Comprehensive Resource of Human Phosphosites within Their Full Context.” JOURNAL OF PROTEOME RESEARCH 19 (8): 3478–3486. doi:10.1021/acs.jproteome.0c00306.
- Vancouver
- 1.Ramasamy P, Turan D, Tichshenko N, Hulstaert N, Vandermarliere E, Vranken W, et al. Scop3P : a comprehensive resource of human phosphosites within their full context. JOURNAL OF PROTEOME RESEARCH. 2020;19(8):3478–86.
- IEEE
- [1]P. Ramasamy et al., “Scop3P : a comprehensive resource of human phosphosites within their full context,” JOURNAL OF PROTEOME RESEARCH, vol. 19, no. 8, pp. 3478–3486, 2020.
@article{8671252, abstract = {{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.}}, author = {{Ramasamy, Pathmanaban and Turan, Demet and Tichshenko, Natalia and Hulstaert, Niels and Vandermarliere, Elien and Vranken, Wim and Martens, Lennart}}, issn = {{1535-3893}}, journal = {{JOURNAL OF PROTEOME RESEARCH}}, keywords = {{Biochemistry,General Chemistry,phosphorylation,PTM,protein structure,proteomics,reprocessing,PHOSPHORYLATION SITES,POSTTRANSLATIONAL MODIFICATIONS,PROTEIN-PHOSPHORYLATION,PROTEOMICS DATA,PREDICTION,SEQUENCE,(MSPIP)-P-2,MECHANISM,SPECIFICITY,UNIVERSAL}}, language = {{eng}}, number = {{8}}, pages = {{3478--3486}}, title = {{Scop3P : a comprehensive resource of human phosphosites within their full context}}, url = {{http://doi.org/10.1021/acs.jproteome.0c00306}}, volume = {{19}}, year = {{2020}}, }
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