Overview of docking procedure with DAIM, SEED, FFLD, and CHARMM

The high-throughput docking approach consists of four consecutive steps:

  1. Decomposition of each molecule of the library into mainly rigid fragments
  2. Fragment docking with evaluation of electrostatic solvation
  3. Flexible docking of each molecule of the library using the position and orientation of its fragments as anchors
  4. LIECE evaluation of the binding free energy for the best poses

The first three steps are performed by in- house-developed computer programs (DAIM, SEED, and FFLD), while CHARMM is used for the energy minimization and finite-difference Poisson calculations in the fourth step.

Publication Link: 
Efficient electrostatic solvation model for protein-fragment docking
In silico discovery of beta-secretase inhibitors
Exhaustive docking of molecular fragments with electrostatic solvation
Fragment-based flexible ligand docking by evolutionary optimization
Link to video file: 
docking_pipeline.mp4