Total Energy
MIX
Assumed pH 7.4
1. Starting structure: Using the poses as described in the PosePredictionProtocol file.
2. Total Energy: kept the whole enzyme fixed while allow everything (the backbone, sidechain, water) within 5 A around the ligand totally relexed, mmffs force filed to energy minimize the complex. Total Energy = Enzyme+Ligand+InteractionEnergy
3. Ranking Score: Rank by Total Energy.
manual generated poses from their bound analog
MIX (in-house software)
Assumed pH 7.4
Starting structure: Ligands were prepared using Schrodinger's standard ligand preparation at pH 7.4. The stereochemistries were given in the isosmiles strings and were therefore kept. Proteins were prepared using Schrödinger.s protein preparation wizard. Bond orders were assigned, hydrogen atoms added, disulfide bonds were generated, and water orientations were sampled. The charge states were kept at pH 7.0. Missing loops and side chains were constructed. The given residue confirmations were kept, with no alternative residue conformations examined.
waters are considered
ligand conformations are considered
no docking or overlay was used. Simply generated the ligand structures from the bound lignad in the crystal complex.