External Resources
PDBi builds on the global Protein Data Bank (PDB) archive and related bioinformatics resources. Below is a curated list of external websites for structural biology, biomolecular data, AI-based predictions, sequence/function annotations, and community tools. These platforms complement PDBi for deeper research, validation, and analysis.
1. Worldwide Protein Data Bank (wwPDB) Consortium
The primary global archive for 3D biomolecular structures. PDBi synchronizes with these partners for up-to-date structural data.
wwPDB – Worldwide Protein Data Bank
Central hub for the PDB archive, deposition guidelines, validation tools, and policies.
https://www.wwpdb.org/RCSB PDB (USA)
Comprehensive search tools, Mol* visualization, PDB-101 educational resources, and APIs.
https://www.rcsb.org/PDBe – Protein Data Bank in Europe
Advanced entry views, PDBe-KB knowledgebase, 3D-Beacons integration, validation reports, and motif searches.
https://www.ebi.ac.uk/pdbe/PDBj – Protein Data Bank Japan
Multilingual interface, Omokage shape similarity search, Molmil viewer, and computed model archives.
https://pdbj.org/BMRB – Biological Magnetic Resonance Data Bank
NMR-specific structural data (chemical shifts, relaxation parameters) integrated with PDB.
https://bmrb.io/2. AI & Structure Prediction Resources
Computational tools that are revolutionizing structural biology in the post-AlphaFold era.
AlphaFold Protein Structure Database
Millions of predicted protein structures from DeepMind and EMBL-EBI.
https://alphafold.ebi.ac.uk/ESMFold / ESM Atlas
Meta AI’s large-scale protein structure predictions and language model-based structural atlas.
https://esmatlas.com/3. Sequence, Function & Classification Resources
Essential databases linking biomolecular structure to biological function and classification.
Gene Ontology (GO) Consortium
Standardized vocabulary for molecular function, biological process, and cellular component. Used within PDBi for functional browsing.
http://geneontology.org/SCOPe – Structural Classification of Proteins (extended)
Hierarchical structural classification of protein domains. Forms the basis of PDBi domain browsing.
https://scop.berkeley.edu/4. RNA & Specialized Structure Resources
RNA 3D Hub
Non-redundant RNA structure datasets, classification, and RNA structural analysis tools.
http://rna.bgsu.edu/rna3dhub/