- Course overview
- Search within this course
- What is PDBe?
- Why do we need PDBe?
- How to access and navigate PDBe?
- How to search the PDB using PDBe?
- Guided exercise 1: Giardia lamlia
- Exercise 1: How do I search PDB for Giardia lamblia?
- Exercise 1: How many proteins are there in the PDB for Giardia lamblia?
- Exercise 1: How many of these proteins function as enzymes?
- Exercise 1: Which part of the cell do these proteins come from?
- Exercise 1: What type of ligands do they interact with?
- Guided exercise 2: Glycolysis process
- Exercise 2: How do I search the PDB for enzymes involved in glycolysis?
- Exercise 2: Are all the 10 enzyme structures that are involved in the glycolytic pathway present in the PDB?
- Exercise 2: What part of the cell do the enzymes belong to?
- Exercise 2: How do I identify the different classes of enzymes (e.g. hydrolase) that participate in glycolysis?
- Exercise 2: How many of them display nucleotide binding activity?
- Exercise 2: Which protein family/families does the enzyme Glucokinase belong to?
- Exercise 2: How do I identify the best representative structure from each of the protein families?
- Exploring a PDB entry
- Summary
- Test your knowledge
- Your feedback
- Learn more
- Get help and support on PDBe
- References
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Integrating protein structure information with its function, taxonomy and sequence
One of the major obstacles of integrating structural databases such as PDBe and protein sequence databases like UniProt is the absence of an up-to-date and well-maintained mapping between corresponding entries.
The Structure Integration with Function, Taxonomy and Sequence (SIFTS) addresses this by integrating data from a number of bioinformatics resources (Figure 7). It is used by major global resources; including PDB and UniProt, allowing the integration of sequence and structure information between resources
The SIFTS project started in 2001 and has resulted in the creation of a robust mechanism for exchanging data between these two primary data resources.