Alignment Tips

Aligning the Molecules

When playing DrgDscvry you are shown two molecules, the Query Molecule (the thin black molecule) and the Match Molecule (the thicker grey molecule). The Query Molecule's shape was determined using crystallography, which is a method to determine a molecule's shape.  However the lab has not tested the Match Molecule, and we do not know it's exact orientation.

For this reason you are able to rotate, translate, and contort the Match Molecule.

The easiest way to do this aligning the molecules by pressing the  Go button in the upper right. 

The Match Molecule will automatically move and rotate it's bonds to try to mimic the Query Molecule. To stop the alignment press the  Freeze  button in the upper right. 

Rubber Bands

Note: Pressing  Go will not necessarily return the best alignment.

Thus players can move the molecules around themselves by using rubber bands. Here are the steps to add a rubber band.

1) Hold your finger down on the screen, a magnifying scope will appear.

2) Drag your finger on top of an atom to put the atom in your scopes. The atom will grow larger. 

3) Hover over the atom until your magnifying scope turns yellow. You have now attached one end of the rubber band.

4) Drag your magnifying scope to another atom. The rubber band will automatically attach. Those two atoms will now be pulled towards each other. Once they have been pulled together the rubber bands will automatically disappear.

Note: The rubber bands will not move the molecule until you press the  Go  button.

Undo/Redo

If you have misplaced a rubber band, the quickest way to remove it is by pressin the Undo button pictured below.

Multiple Rubber Bands

To contort the Match Molecule you will need to add multiple rubber bands. The easiest way to do this is first holding the alignment by pressing the  Freeze  button (if it is not already pressed). Then add as many rubber bands as you want. Then press the  Go  button.

Stream Help

Communicating your insights to other citizen scientist is incredibly important for scientific discovery. In DrugDiscovery players communicate using Twitter. All tweets that mention @DrgDscvry appear in game in the @DrgDscvry Stream:

Note: All tweets from the game are pre-populated to be tweeted at @DrgDscvry and thus will not spam your followers twitter streams.

Twitter is integrated into the game in two amazing ways:

1. Pressing a tweet with a molecule hashtag, such as #CA0001, will load that molecule into the game.
2. Pressing a tweet with a tiny url such as http://t.co/Fey99B! downloads an alignment that another player uploaded.

Twitter Details

By pressing on the blue indicator button, you will see the Tweet Details page.

1. There you can reply to the tweet.
2. Award the sender Insight Points (by tweeting @ them #DrgPoints)
3. View the Molecule

Mission Help

Every week a new mission will be posted to the Mission Blog Page.

On the mission tab in the app you can:

1. Open up the Mission Blog Page
2. See Mission tweets that summarize the current mission.
3. Load any two molecules into the game by clicking on "Molecule Databases"

Molecule Databases

When you click on Molecule Databases you can load any Query and Match molecules into the game.

First select a molecule database.

Then select the specific molecule that you would like.

Then repeat the process for the Match molecule. 

Profile Help

Leaderboard

High Schoolers

1. @myelbows - 570

Elementary Schoolers

1. @alimpaecher - 270

"Tweet Stats" to get aded to the Leaderboard!

Point Types

There are four types of points in DrugDiscovery:

1. Experience Points
• You earn experience points for everything you do on the site. Experience points help you level up!
2. Voting Points
• You earn these by playing the voting game.
3. Tweeting Points
• You earn these by tweeting your insights.
4. Insight Points
• Other players award you insight points for insightful tweets.

Voting Game Help

This post explains how to play the Voting game in DrugDiscovery.

Basic Gameplay

1. Choose Query Molecule and a Match Molecule.
2. Vote on whether you believe the two molecules are chemically similar.
3. Tweet your insights!

GamePlay Details

In the voting game you will be comparing two molecules:
1) Query Molecule: The thinner black molecule has been shown in lab studies to influence diseases (such as Alzheimer's and Cancer). It does this by binding with proteins, which either activates or inhibits the proteins. These Query Molecules, however, cannot be used because they are toxic.

2) Match Molecule: The thicker gray molecule, unlike the Query Molecule, is non-toxic. Thus if it has a similar chemical make-up as the Query Molecule, it may be a cure for a disease.

If you think the Match Molecule has a similar chemical makeup press the Checkmark, otherwise press the  X .

Starting the Game

To start the game press on the "Voting Game" tab. There you will see eight toxic Query Molecules. Select one.

You will then be presented with around 30 possible Match Molecules. Select one to begin the game.

Once you are in the game press the info button in the lower right to have the option to return back to the menu:

Info Button

Lab Tested

In the voting game, we have actually tested the Match Molecules in the lab and know whether they bind with the same protein as the Query Molecule. Thus we can provide instant feedback on whether your vote was correct.

One frequently asked question is: "How do I know what to vote for? What makes two molecules chemically similar?"

The answer to this is not entirely understood, and that's why we created the "Voting Game"! If you begin to see a pattern of what binds and what doesn't bind, tweet your insight!

Alignment

In the voting game we know the shape of the Query Molecule. The 3D structure it has in the game is the shape it takes when binding with a protein.

Alternatively the Match Molecule's shape is not set. You can rotate, translate, and contort it. This will give you insight into whether the two molecules have a similar chemical structure. The Match Molecule will naturally try to find the best alignment, however you can guide it using rubber bands.

To learn how to best align two molecules read the Alignment Tips post.

Current Mission!

Mission 1

Query Molecule: #WT1763, a Nucleoside Reverse Transcriptase Inhibitor known as Stavudine

Match Molecule:  #WT1370, #WT1374, #WT1413,  and #WT1857
Target Disease: HIV

Mission Objective: Find which of the match molecules will act as a Nucleoside Reverse Transcriptase Inhibitor by comparing it to Stavudine. Tweet your answers and insights.

Mission Details:

Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS).  When the virus infects a person, it weakens the person’s immune system and makes them susceptible to other infections and cancers.  In fact, a person with AIDS generally will die from a secondary disease, and not AIDS itself, because their body can’t fight off the new infection. (http://en.wikipedia.org/wiki/HIV)

One of the key steps of HIV infection is the ability for the virus to get its genetic information into a host cell.  To do this, the virus uses a protein called Reverse Transcriptase (RT) to turn its RNA into DNA.  This DNA can then insert into a human cell’s own DNA and cause the cell to start making new viruses.  Nucleoside reverse transcriptase inhibitors (NRTIs) are drugs which can help stop HIV by preventing the elongation of the newly synthesized DNA.  Since NRTIs look a lot like normal DNA bases, they get incorporated into the DNA chain.  However, NRTIs lack key chemical groups which allow the DNA to keep elongating, so the DNA just falls off and is unable to be used for virus replication. (http://en.wikipedia.org/wiki/Nucleoside_reverse_transcriptase_inhibitors)

One Nucleoside Reverse Transcriptase Inhibitor is Stavudine, which can be found in the commercial product Zerit. (#WT1763).  Unfortunately, resistance to Stavudine has been reported, arising from mutations in HIV RT.  To stay ahead of the disease, we need to find drugs which will not suffer from resistance.

We have 4 additional molecules which may also be a Nucleoside Reverse Transcriptase Inhibitor:
#WT1370
#WT1374
#WT1413,
and #WT1857


By comparing these molecules to Stavudine, which of these molecules do you think may help cure HIV?

Make sure to tweet your answer and insights!

DrgDscvry