ArticleProtein science : a publication of the Protein Society2019
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins.
Article in Protein science : a publication of the Protein Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Machine learning-driven prediction of substrates for enzymes introducing or removing protein post-translational modifications.Communications chemistry · 2025Article
- Optimal Descriptor Subset Search via Chemical Information and Target Activity-Guided Algorithm for Antimicrobial Peptide Prediction.Journal of chemical information and modeling · 2025Article
- Machine learning for antimicrobial peptide identification and design.Nature reviews bioengineering · 2024Article
- Examining evolutionary scale modeling-derived different-dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow.Protein science : a publication of the Protein Society · 2024Article
- Machine Learning Methods in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Inhibition of Pertussis Toxin by Human α-Defensins-1 and -5: Differential Mechanisms of Action.International journal of molecular sciences · 2023Article
- An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling.Computational and structural biotechnology journal · 2023Review
- ABP-Finder: A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria.Antibiotics (Basel, Switzerland) · 2022Article
- Antimicrobial peptides with cell-penetrating activity as prophylactic and treatment drugs.Bioscience reports · 2022Review
- PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity.Journal of proteome research · 2022Article
- Computational Design of Inhibitors Targeting the Catalytic β Subunit ofAntibiotics (Basel, Switzerland) · 2022Article
- Machine learning methods for protein-protein binding affinity prediction in protein design.Frontiers in bioinformatics · 2022Article
- Article
- Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach.Scientific reports · 2020Article
- Protein-Protein Interactions Efficiently Modeled by Residue Cluster Classes.International journal of molecular sciences · 2020Article
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins.Protein science : a publication of the Protein Society · 2019Article
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4 authors.
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Abstract
Computational tools for the analysis of protein data and the prediction of biological properties are essential in life sciences and biomedical research. Here, we introduce ProtDCal-Suite, a web server comprising a set of machine learning-based methods for studying proteins. The main module of ProtDCal-Suite is the ProtDCal software. ProtDCal translates the structural information of proteins into numerical descriptors that serve as input to machine-learning techniques. The ProtDCal-Suite server also incorporates a post-processing optional stage that allows ranking and filtering the obtained descriptors by computing their Shannon entropy values across the input set of proteins. ProtDCal's codification was used in the development of models for the prediction of specific protein properties. Thus, the other modules of ProtDCal-Suite are protein analysis tools implemented using ProtDCal's descriptors. Among them are PPI-Detect, for predicting the interaction likelihood of protein-protein and protein-peptide pairs, Enzyme Identifier, for identifying enzymes from amino acid sequences or 3D structures, and Pred-NGlyco, for predicting N-glycosylation sites. ProtDCal-Suite is freely accessible at https://protdcal.zmb.uni-due.de.
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