Create a structure-based combinatorial library for sarin (repeat of exercise 6 in PubChem Basics)
Create a function-based combinatorial library for sarin (repeat of exercise 7 in PubChem Basics)
Using the Entrez History, find compounds common to both libraries, identify the number of unique
compounds, and created a combined library
Create structural cluster diagrams of the various sarin combinatorial libraries
Steps
Create a structure-based library for sarin
Complete Exercise 9 in PubChem Basics. (If you have already completed this
exercise, the results should be in your Entrez History.)
Create a function-based library for sarin
Complete Exercise 10 in PubChem Basics. (If you have already completed this
exercise, the results should be in your Entrez History.)
Locate the sarin libraries on your Entrez History
From the NCBI home page, select PubChem Compound from the Database
menu, and click Go (with a blank query).
Click the History tab.
Identify the number corresponding to the structure-based library (Select xxx document(s) where xxx is the number of records retrieved by the structure search in step 1).
Identify the number corresponding to the function-based library (PubChem Compound with MeSH Links for MeSH
(Select 82002800)).
Identify compounds common to both libraries
Enter a query consisting of the numbers of the two libraries, each preceded with a # and separated by AND (eg. #3 AND #6).
Click Preview.
How many compounds do the two libraries share in common?
Identify compounds present in only one of the two libraries
Enter two queries, each consisting of the numbers of the two libraries preceded with a # and separated by NOT (eg. #3 NOT #6).
Click Preview to execute each query.
How many compounds were found only by the structure similarity method?
How many compounds were found only by the MeSH terms?
Create a combined library from the two libraries
Enter a query consisting of the numbers of the two libraries preceded with a # and separated by OR (eg. #3 OR #6).
Click Preview.
Why is the size of this library not the sum of the sizes of the two component libraries?
Cluster the compounds in each library by structural similarity
You should now have three libraries: a structure-based library, a function-based library, and the combination of these two.
Choose one of the three libraries, and click on the number of records to the right of its History query key.
Click PubChem Structure Clustering from the Display menu.
To collapse or expand the tree to show a different number of clusters, click on the Tanimoto score axis at the desired branching limit.
At the top of the page, click the Show Structures button to show representative structures of each cluster.
Compare the structural diversity of the three libraries
Repeat the previous step for the other two libraries.
Which of the libraries has the most diverse group of structures?
