Schrödinger Docking Tutorial
Schrödinger is a complete software package for drug discovery, including: induced fit and flexible docking mode based on receptor and ligand structure; docking mode based on receptor structure and ligand polarity; based on receptor structure and solution environment properties Docking mode of combinatorial chemical library; combinatorial chemical library design and docking mode based on combinatorial library; drug design based on ligand structure, pharmacophore and 3D-QSAR; biomolecular structure simulation, protein, sugar, nucleic acid, small peptide, etc.; based on target Drug design; ADME properties prediction. How does Schrödinger do molecular docking? The following provides Schrödinger molecular docking tutorials, I hope I can help you.
Tutorial
For docking, two files are needed: a protein grid and a ligand library.
Tools are provided by Schrödinger Inc. for preparing both. One important tool in the Schrödinger suite is Maestro. It can be downloaded as part as an Academic Campaign (http://www.schrodinger.com/freemaestro/) and is also useful for post-processing.
Before making the grid, the protein must be prepared (proteins from the Protein DataBank sometimes miss some atoms for example).
Then, you need a ligand library. How to prepare it depends and what you want to dock and what you already have. Schrödinger Inc. provides a software called ligprep for preparing the ligands. It can read a lot of input file formats and convert them to 3D, add the missing hydrogens, adapt the ionization state and minimize it.
Once you have the grid and the ligands, you can start the docking. The easiest way of doing it is by directly using glide. The command is: glide -WAIT InputFile.in. Again, I use the -WAIT option. Glide only needs an input file which looks like this:
EPIK_PENALTIES NO
USECOMPMAE YES
WRITEREPT YES
NREPORT 15000
RINGCONFCUT 2.500000
PRECISION HTVS
GRIDFILE glide-grid.zip
LIGANDFILE File.mae
The first one can be opened by Maestro to see the poses of the ligands. It is in fact a .mae file which is zipped. So if you want to read it, you can rename it to InputFile_pv.mae.gz and then gunzip it.
The .rept file is a text file which is written only if you have asked WRITEREPT YES in the input file and summarizes the results with the scores. If you have splitted your docking jobs and want to merge them, you can use the following command in which the 20 best poses will be written in NewFile.rept and NewFile_pv.maegz: $SCHRODINGER/utilities/glide_merge -r NewFile.rept -o NewFile_pv.maegz -n 20 OldFile_pv.maegz
If you don't have a lot of ligands, you can use the precedent procedure directly with the XP precision.
* For Research Use Only.
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