C371 Exercise 5: Molecular Visualization and 3D Searching
Updated: 8 November 2004
1. Use the Cambridge Structural Database to work through Tutorials 4
(3D Substructure Search) and 6 (Pharmacophore Search) on computers 5-9 in the
Chemistry Library at IUB or in the IUPUI Department of Chemistry Computational
Molecular Science Facility.
[ ] I successfully completed the assigned tutorials.
2. Download the file
Use the Mercury program to view the file, but uncheck the box to Show hydrogens.
(Mercury is available on computers that have
the Cambridge Structural Database or as a free download at:
Did it work? If not, why?
Now view the file in ChemOffice's Chem3DPro. (It is NOT on the STC computers.)
you can download the ChemDraw Ultra program to your own computer (not an STC
computer) by creating a CambridgeSoft user
account and installing ChemDraw Ultra (which includes Chem3DPro) at:
Choose the model type "Ribbons," then, under the Tools menu, magnify the
object until you can clearly see the small molecules depicted. Grab the
rotate tool in the left column (arrow with a circle around it), and rotate it
around all three axes.
While in the program, note the many options to work with the molecule.
[ ] I have completed this part of the assignment.
3. Not long ago a subscriber to CHMINF-L had a question about the CAS Registry
Number for a compound for which he had only the SMILES code. It turned out to
be 4-(4-pyridinyl)-bezeneamine (RN: 13296-04-3). Find the compound using
SciFinder Scholar, and print out the full record for the compound.
Return to the previous window in SciFinder Scholar, view the molecule
in ViewerLite (hit the water molecule icon), and save the file from ViewerLite
as an MDL MOL file.
Using the Cambridgesoft ChemOffice program Chem3DPro, open the file.
Did it work?
4. Using the SMILES code NC1=CC=C(C2=CC=NC=C2)C=C1
connect to CORINA at:
Input the SMILES code, give it the identifier (name) corina_bezeneamine, and
Generate the 3D
structure. Does it look correct on your screen?
Now save it as a WebLab Viewer Pro sdf type. Open Accelrys ViewerLite and
view the molecule. Does it look correct now?
5. Read the brief article in C&EN on 3D models produced with Rapid Prototyping Technology.
It uses PDB (Protein Data Bank) data to create the model of biomolecules
(a 3D model that you can hold in your hands)
by means of 3D printing technology,
This web page has pictures of the products:
[ ] I have read the article and looked at the models.