Build Model uses an original graph-theoretical approach5 to assign optimal ionization states of protein residues at arbitrary pH conditions, which is based on the Screened Coulomb Potential (SCP) model.5,6
After completing protein preparation, an energy grid map (Stage 2) is calculated and saved for the protein binding site. This energy map is then used to dock the ligand structures.
The docking engine in Lead Finder (Stage 3) combines a genetic algorithm search with local optimization procedures, which make Lead Finder efficient in coarse sampling of ligands poses and following refinement of promising solutions.
The standard docking mode provides an accurate and exhaustive search algorithm. However, in extra-precision mode, Lead Finder uses the most rigorous sampling and scoring algorithms to increase accuracy and reliability of predictions at the cost of slightly slower speed of processing.