- Course overview
- Search within this course
- What is PDBe?
- Why do we need PDBe?
- When to use PDBe?
- How to access and navigate 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
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Case study 1: Narrowing down your search results
Task: Search for ‘Human rhinovirus 14’ from ‘Rossmann MG’.
Adding new parameters to an existing search will help to refine the query and narrow down your search results.
If you wish to further refine the query based on the author name that you have searched before (Figure 21), you can use the filters on the left-hand side on the results page (Figure 22) or advanced search (Figure 23) instead of going back and starting over again.
a) Using filters – in a filter panel go to ‘Macromolecules’ and under the ‘Organism name’ tab you can find ‘rhinovirus 14’ (highlighted in blue, Figure 23)
b) Using advanced search – opening the ‘Advanced search’ (Figure 24) and clicking on ‘Select to add a search field’ (highlighted in yellow) you can search for ‘Organism name’ in the menu and then fill out ‘ human rhinovirus 14’ to refine your search
Note: After picking the category based on what you want to filter your search in the ‘Select to add a search field’, there is also a possibility to define the conditions. You can use ‘AND’, ‘OR’ or ‘NOT’ to change the query.
Eg: If you are interested in Rossmann MG structures but want to exclude those from Rhinovirus 14 as a source organism, you can use ‘NOT’ to define that.
In both cases you get the list of 29 entries where the author is Rossmann MG and source organism is Rhinovirus 14.
