Screen saver/Graphics: FightAIDS@Home – What are the colored spheres in Panel A?
The search algorithm used in AutoDock is not just looking at one possible solution of one candidate drug molecule (ligand) but is actually evaluating many possible solutions at once. The spheres show places where the best drug molecule to HIV-1 protease dockings have been calculated and the color shows how good they are. AutoDock is trying to find the best way that the current ligand, the one your agent has downloaded, can fit together with the target HIV-1 protease. You can think of the ideal drug we are trying to find as a “key,” and the HIV-1 protease as a “lock.” Unlike keys in the real world, however, many drug molecules bend to change shape. In this respect, molecules are like a dancer’s body; the same body is able to adopt many different poses and shapes. Unfortunately, we do not know what shape a candidate drug will adopt until we try millions of different possibilities and then select the best one. To find the best fit, we are using an algorithm. An algorithm is just a recipe,
