Boris Depoortere
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Boris Depoortere has a total of 7 co-authors. Here are the top co-authors by number of shared publications:
- Adrián Díaz
Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
1 shared publication - Lennart Martens
Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
1 shared publication - Natalia Tichshenko
CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
1 shared publication - Pathmanaban Ramasamy
CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
1 shared publication - Paul De Geest
VIB Data Core, VIB Technologies, VIB, Ghent, Belgium
1 shared publication - Rafael Andrade Buono
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
1 shared publication
Latest Publications
- Open Access
Scop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein function
Post-translational modifications (PTMs) and genetic variants regulate protein function, signalling, and disease, but their interpretation requires integration of sequence annotations with structural, interaction, and biophysical context. Although resources such as Scop3P, UniProt, the Protein Data Bank, and AlphaFold provide extensive annotations and structural information, integrating these data into reproducible structure-aware analyses still requires custom scripting and manual coordination between multiple independent tools. To address this challenge, we developed Scop3P-Toolkit , an open-source executable analytical environment for interactive analysis of PTMs, mutations, and proteomics-derived peptides in their structural context. The toolkit integrates protein annotation retrieval with structural mapping, residue interaction network analysis, comparative structural analysis, and residue-level biophysical profiling within a unified framework. Experimentally supported phosphosites, phosphopeptides, and phosphoproteomics evidence are provided for human proteins through Scop3P, with optional integration of curated UniProt PTM annotations. UniProt-derived PTMs, sequence features, and genetic variants are available for proteins from any species, extending the framework beyond the human phosphoproteome. Scop3P-Toolkit supports structure-centric analyses including interpretation of PTMs and disease-associated variants, analysis of residue interaction networks and their rewiring across alternative conformations, structural localisation of peptides, and exploration of protein–protein, protein–ligand, and host–pathogen interfaces. Interactive visualisation links sequence annotations, three-dimensional structures, residue interaction networks, and biophysical profiles, enabling coordinated exploration across multiple molecular representations. The toolkit is distributed as Jupyter notebooks, browser-based Voilà applications, and a Galaxy interactive tool, providing transparent, accessible, and reproducible workflows for both computational and experimental researchers. By integrating biological annotation resources into executable, structure-aware workflows, Scop3P-Toolkit enables reproducible interpretation of PTMs, mutations, and proteomics data.
Open AccessScop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein function
Post-translational modifications (PTMs) and genetic variants regulate protein function, signalling, and disease, but their interpretation requires integration of sequence annotations with structural, interaction, and biophysical context. Although resources such as Scop3P, UniProt, the Protein Data Bank, and AlphaFold provide extensive annotations and structural information, integrating these data into reproducible structure-aware analyses still requires custom scripting and manual coordination between multiple independent tools. To address this challenge, we developed Scop3P-Toolkit , an open-source executable analytical environment for interactive analysis of PTMs, mutations, and proteomics-derived peptides in their structural context. The toolkit integrates protein annotation retrieval with structural mapping, residue interaction network analysis, comparative structural analysis, and residue-level biophysical profiling within a unified framework. Experimentally supported phosphosites, phosphopeptides, and phosphoproteomics evidence are provided for human proteins through Scop3P, with optional integration of curated UniProt PTM annotations. UniProt-derived PTMs, sequence features, and genetic variants are available for proteins from any species, extending the framework beyond the human phosphoproteome. Scop3P-Toolkit supports structure-centric analyses including interpretation of PTMs and disease-associated variants, analysis of residue interaction networks and their rewiring across alternative conformations, structural localisation of peptides, and exploration of protein–protein, protein–ligand, and host–pathogen interfaces. Interactive visualisation links sequence annotations, three-dimensional structures, residue interaction networks, and biophysical profiles, enabling coordinated exploration across multiple molecular representations. The toolkit is distributed as Jupyter notebooks, browser-based Voilà applications, and a Galaxy interactive tool, providing transparent, accessible, and reproducible workflows for both computational and experimental researchers. By integrating biological annotation resources into executable, structure-aware workflows, Scop3P-Toolkit enables reproducible interpretation of PTMs, mutations, and proteomics data.