CADD course learning (8) -- virtual screening of Compound Library

CADD Course study （8）-- Virtual screening of Compound Library （Virtual Screening）

PyRx： be based on AutoDock Virtual filtering software for

Virtual screening

Virtual screening , Also known as computer filtering , That is, before biological activity screening , Pre screen compound molecules on the computer , To reduce the number of compounds actually screened , At the same time, improve the discovery efficiency of lead compounds

PyRx： Install well PyRx after , You need to install the previously installed autodock4.exe and autogrid4.exe Two files cannot be found PyRx Installation directory , To ensure that PyRX Smooth operation in the local .

PyRx Key steps of virtual screening ：

1. utilize AutoDock Wizard Prepare the receptor grid file
2. utilize Open Babel Prepare ligand small molecules
3. utilize Vina Wizard Perform virtual filtering
4. Virtual screening result analysis
   

PyRx Key steps of virtual screening ：

1. utilize AutoDock Wizard Prepare the receptor grid file





2. utilize Open Babel Prepare ligand small molecules

Save results

4. Virtual screening result analysis
Virtual filter results can also be found in the following directory ,pdbgt Format files can be imported Pymol
C:\Users\Administrator.mgltools\PyRx\Macromolecules\1EP_pra

practice ：

from PDB Download... From the database 1IEP Crystal complex , And download a small molecule library file （ Build or ZINC download ）, utilize PyRX Complete virtual screening practice , And analyze the results .

Others conclude

If the ligand molecule is small and the protein molecule is large , When you are not sure where the small molecules dock , Enlarge the lattice for blind docking , Ligand small molecules may dock at multiple places in the protein , Just use 1.MOE Look for sites ;
2. Cluster analysis evaluates the docking results ;
3. Search the literature to find important amino acids for docking ;
4. Virtual screening is used to evaluate the docking results of small molecule library

Supplementary content

file sdf,df,mod2 Does the format file contain multiple molecules , How to split a single molecule

vina_split.exe --input a.pdbqt