The proposed multiple grid arrangement method was implemented in Glide by modifying a cross-docking script for Glide, xglide.py.py
To analyze the docking results, python scripts in MGL tools package were used for visualization.
Individual PDB files were prepared for docking using the prepare_ligand4.py script from MGLTools 1.5.4 [20], using only the largest non-bonded fragment present.
When using MOLA-AD4, dpf files for each compound are created (dpf is need for docking with AutoDock4) using the Python script "prepare_dpf4.py" available on ADT.
The screening was driven by a script that runs the docking of several ligands on a cluster of CPUs in parallel, allowing the full screening to be completed in a couple of weeks.
It means that writing the script to launch the docking is a complex task, which may not be immediately successfull.
A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size.
A simulated annealing script, appropriate for NOE-driven docking, was derived from the Xplor-NIH example script, gb1-anneal.py.py
The model hSR-AI structure and either the human apo A-I structure (PDB entry 2a01) or the human apo E structure (PDB entry 1ea8) were docked together using the suite of Haddock scripts (31), with constraints on docking residues of SR-A as follows: Arg325, Lys332, Lys335, and Lys338.
Parameter files were generated for the ligands using the utility script hetgrp_ffgen (Schrodinger Inc .. PRIME docking then built the ligand from the core fragment in an arbitrary conformation in the active site.
Python scripts are written to automate the docking, the probability calculation and the peptide sequence determination procedures.
