| PDB | • Protein Data Bank |
| PDBe | • Protein Data Bank in Europe |
| * APIs for Molecular Structure Databases |
| Anatomy and Taxonomy of Protein Structure |
| BMRB | Biological Magnetic Resonance Data Bank |
| CCD | Chemical Component Dictionary |
| PDBeChem | Chemical Components in the PDB (ligands, small molecules) |
| Dali Database of structural neighbours |
| CoDNaS | Database of Conformational Diversity of Native State in proteins |
| Database of Macromolecular Movements |
| DisProt | Database of Protein Disorder |
| DBAli | Database of Structure Alignments |
| MobiDB | Database of protein disorder and mobility annotations |
| Pfam | Database of protein families and hidden Markov models (HMMs) |
| DSSP | Definition of Secondary Structure of Proteins given a set of 3D coordinates |
| PDB-101 | Educational Portal of Protein Data Bank |
| EMDB | Electron Microscopy Data Bank |
| CATH | Hierarchical domain classification of protein structures in the Protein Data Bank (PDB) |
| ModBase | Homology Modeling: Database of Comparative Protein Structure Models |
| SWISS-MODEL | Homology Modeling: Database of three-dimensional comparative protein structure models |
| PMP | Homology Modeling: Protein Model Portal |
| Introduction to Protein Data Bank Format |
| Iridium: Protein-Ligand Structure Database |
| JenaLib | Jena Library of Biological Macromolecules |
| Molecular Graphics Visualization Software |
| NCBI Structure Database |
| NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers |
| NDB | Nucleic Acid Database |
| PDB File Format Documentation |
| PIRSF | PIR Super Family Classification System |
| PDBsum | Pictorial database of 3D structures in the Protein Data Bank |
| PDBj | Protein Data Bank Japan |
| CASP | Protein Structure Prediction Center |
| Proteopedia |
| SUPERFAMILY database of structural and functional annotation for all proteins |
| SBKB | Structural Biology Knowledgebase |
| Structural Biology Software Database |
| SCOPe | Structural Classification of Proteins - extended |
| SCOP2 | Structural Classification of Proteins 2 |
| SFLD | Structure-Function Linkage Database |
