Teaching Points for Virtual Screening 2 lab


VDS Staff,

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

There are 4 GOLD runs to the lab

Human DHFR:   1st Run and 2nd Run

Anthrax bacterial DHFR: 1st Run and 2nd Run

 

We want to make sure they aren’t all on the same blades (slower). So, we will help them select which blade to use based on the $ganglia cpu_user command.

Have them choose an empty blade on the upper deck (#8-15)

Using only 2 processors per run.

 

They are NOT making images for every ligand – only a few.

When they search for the Lipinski’s data on www.hit2lead.com – they can input ALL of the ligand numbers at once (instead of doing it one by one)

 

TROUBLESHOOTING:

The gold.hosts file  – make sure it is not on blade #13  – which is dead!

Editing the configuration files – make sure they have the EXACT letters and capitalization

IMPORTANT CONCEPTS:

The anthrax enzyme is very similar to the human version in 3-d structure

 

The mtxfor1u72.mol2    is the ORIGINAL ligand that is used to define the active site

 

The ‘&’ at the end of $goldremoteP 2 gold.conf &    is to run the job in the background.

 

A ligand database can have thousands of molecules in it that are either very similar – or very different. These ligand came from the Chembridge Kinase library that has similar ligands that are supposed to work well against kinase enzymes.

 

Most of these compounds will satisfy Lipinski’s rules – because we buy them from a company that is trying to make drugs for humans.

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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