Teaching Points for Virtual Screening 1 Lab


VDS Staff,

The notebook for this one is not due until after  VS2 lab. But there is a Lab Report due for this one next week.

You should recommend that they comment in their Word document as they go.

 

There are 2 parts to the lab

PART 1: PyMol analysis of Xray poses

PART2: GOLD docking and subsequent analysis of docked poses

 

It is recommended that you guys help them set up their GOLD jobs first (Part 2). Students should be getting into a groove with PyMol now. So, they should be able to do Part 1 on their own for the most part.

 

They will create a set of figures for EACH part and then put them together side-by-side to compare them for the writeup. (in total they will have about 32 + images). In order for them to make the images quickly – they need should not be ‘tweaking’ their protein each time.

 

TROUBLESHOOTING:

When they first login to the DDFE, it may ask them for a filename – they should just hit ENTER.     It may then ask them for a passphrase:  they should just hit ENTER

 

The gold.hosts file

When they run the GOLD run they need the gold.hosts file. If this is not in their directory, you will have to help them go to the /home/chem204 directory and run the command:

$sh copyhosts.sh          #don’t re-type the $   it is already at the start of the line.

 

This will put the correct file into their folder (it gives them lots of error messages – but the file should still pop up in their folder)

 

IMPORTANT CONCEPTS:

The DDFE is on the 5th floor of Welch

A pose is one possible way a ligand can fit (GOLD tests out many different conformations)

The Xray crystal poses may not match the GOLD poses.

A high score in GOLD does not necessarily mean the pose is right or the ligand is a good one

 

IMPORTANT SKILLS:

Understanding  file structure in Linux operating environment and how to move around in the directories

Creating a list in Excel that is sortable and each of the columns are in separate cells (Bestranking.lst)

 

 

 

 

 

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