67a3e-FreeEnergyProtocol.txt

Name

Total Energy

Software

MIX

Parameters

Assumed pH 7.4

Method

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.

67a3e-PosePredictionProtocol.txt

Name

manual generated poses from their bound analog

Software

MIX (in-house software)

System Preparation Parameters

Assumed pH 7.4

System Preparation Method

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.

Pose Prediction Parameters

waters are considered
ligand conformations are considered

Pose Prediction Method

no docking or overlay was used. Simply generated the ligand structures from the bound lignad in the crystal complex.