RIDGE (Rapid Docking GPU Engine) performs GPU-based structure-based screening of prepared ligand conformers. Read more here.
To run RIDGE:
- Set up a docking project.
- Go to Docking/Run RIDGE HTD VLS
- Select the conformer database in .molt format you wish to screen. You can download pre-prepared databases here. or prepare your own molt database using the options in Chemistry/Generate Conformers.
- Select a RTCNN score cutoff - it is recommended to undertake a test screen to see what score distributions you will obtain for your receptor.
- Use the default clash weight penalty of 20 unless a validated workflow requires another value.
- You can choose to also evaluate the physics-based score.
Advanced options:
- Clash van der Waals scale (default = 0.82)
- Select a random subset to screen and enter the size of the subset.
- Define the GPU ID number.