- Course overview
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- What information does a PDB entry contain?
- How is the information structured?
- PDB entry overview
- Citation page
- Function and Biology
- Is the protein an enzyme?
- What specific biological processes are associated with the proteins?
- Which sequence family does the protein belong to?
- What protein signatures can be found in the structure?
- What are the structural folds/domains present in the proteins from this entry?
- The SCOP classification of protein folds
- Structure analysis
- Detailed structure analysis
- How can I interactively explore the protein and DNA molecules present in the entry?
- Which amino acids from the protein chain participate in binding interactions with ligands?
- What is the build quality of the protein chain?
- What are the signature domains/folds – Pfam
- What are the signature domains/folds – CATH
- What are the signature domains/folds – SCOP
- What are the probable quaternary structures and biological assemblies?
- Unravelling the symmetry of a virus capsid using assembly information
- Ligands and Environments
- Downloading data from a PDB entry page
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Recommended online courses
- Biomacromolecular structures: An introduction to EMBL-EBI resources
- PDBe: Searching the Protein Data Bank – this course will show you how to search and navigate the PDBe resource
- Searching with the PDBe API – recorded webinar
- PDBeFold: Searching for structural homologues of a protein
- PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure
- PDBeChem: Searching for small molecules and small molecule fragments
Recommended reading
- Varadi, M. et al. (2022) PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Science. 31(10:e4439
- Velankar, S. et al. (2016) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Research. 4(D1):D385-95.