PDBe-KB
PDBe-KB integrates functional and biophysical annotations with macromolecular structure data from the Protein Data Bank (PDB) to contextualize structural data within biological frameworks.
Key Features:
- Standardized data exchange formats: Develops and uses standardized data exchange formats for integrating annotations.
- Integrated knowledge graph: Constructs an integrated knowledge graph linking PDB entries with diverse functional annotations.
- Predicted covalent binders: Includes annotations for predicted covalent binders.
- Phosphorylation sites: Includes annotations for phosphorylation sites.
- Effects of mutations on protein structure: Provides annotations describing effects of mutations on protein structure.
- Energetic local frustration metrics: Provides energetic local frustration metrics as annotations.
- Superposition service: Generates clusters of superposed protein chains across the entire PDB archive on a weekly basis.
- Bulk download service: Provides a bulk download service for large-scale data retrieval.
Scientific Applications:
- Structural contextualization: Contextualize macromolecular structures within biological frameworks using integrated annotations.
- Comparative structural analysis: Enable comparative structural analyses using weekly superposition clusters.
- Covalent binding and PTM analysis: Analyze predicted covalent binders and phosphorylation sites to investigate chemical modifications and binding-related features.
- Mutation impact assessment: Assess effects of mutations on protein structure.
- Functional site analysis: Investigate macromolecular function and interactions using energetic local frustration metrics.
- Large-scale structural analyses: Support large-scale structural analyses and data retrieval via the bulk download service.
Methodology:
PDBe-KB develops standardized data exchange formats, constructs an integrated knowledge graph enriched with functional annotations, generates weekly clusters of superposed protein chains across the PDB, and provides a bulk download service.
Topics
Details
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Mac, Linux, Windows
- Added:
- 4/9/2022
- Last Updated:
- 4/9/2022
Operations
Data Inputs & Outputs
Aggregation
Inputs
Publications
Varadi M, Anyango S, Armstrong D, Berrisford J, Choudhary P, Deshpande M, Nadzirin N, Nair SS, Pravda L, Tanweer A, Al-Lazikani B, Andreini C, Barton GJ, Bednar D, Berka K, Blundell T, Brock KP, Carazo JM, Damborsky J, David A, Dey S, Dunbrack R, Recio JF, Fraternali F, Gibson T, Helmer-Citterich M, Hoksza D, Hopf T, Jakubec D, Kannan N, Krivak R, Kumar M, Levy ED, London N, Macias JR, Srivatsan MM, Marks DS, Martens L, McGowan SA, McGreig JE, Modi V, Parra RG, Pepe G, Piovesan D, Prilusky J, Putignano V, Radusky LG, Ramasamy P, Rausch AO, Reuter N, Rodriguez LA, Rollins NJ, Rosato A, Rubach P, Serrano L, Singh G, Skoda P, Sorzano COS, Stourac J, Sulkowska JI, Svobodova R, Tichshenko N, Tosatto SCE, Vranken W, Wass MN, Xue D, Zaidman D, Thornton J, Sternberg M, Orengo C, Velankar S. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Research. 2021;50(D1):D534-D542. doi:10.1093/nar/gkab988. PMID:34755867. PMCID:PMC8728252.