What effort value should I use for ligand docking?

[Andrew Orry]

Q.What effort value should I use for ligand docking?

A.

When you send the docking job to run using Run Docking/VLS Batch you will notice an 'effort' parameter sometimes also referred to as 'thoroughness'. This value represents the length of the docking simulation - time is roughly proportional to effort. The parameter reflects an inevitable compromise between speed and accuracy but note that timing is strongly dependent on flexibility and size of ligand - by nature a larger flexible ligand requires more time for adequate sampling than a small rigid one.

Some recommendations for choosing an effort value:

• A setting of 3. is our recommended value for docking, we normally benchmark accuracy at this effort level.
• A setting of 1. works well for large Virtual Ligand Screening (VLS) runs.
• When convergence is critical we would recommend to use 10.
• When constraints are used generally lower 'effort' is acceptable.
• When incorporating receptor induced fit by 4D Docking or Explicit Group Docking we would recommend an effort parameter >20.