Help for structure-based virtual screeing

Python Prescription - Virtual Screening Tool

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Help for structure-based virtual screeing

Postby aneeshcna » Mon Feb 03, 2014 10:16 am

Dear users,

I am new with PyRx and virtual screeing. I have installed PyRx in my Ubuntu 32-bit systems and also download sdf file of lead compounds from NCIDS database. The single sdf file contains multiple compounds (1986 compounds). As per the informations from different screncasts and blog from PyRx website, the oversall idea I got about how to do structrue-based virtual screeing with PyRx is listed below.

1. Prepare the pdbqt file for protien of interest
2. Convert ligands sdf file to pdbqt file.
3. Generate grid for the site (acvite site) of interest in the protein, where you want to dock the ligand ( run autogrid)
4. Run the auotdock and alalyze the result.

Am I going on the right direction? If yes, please hlep me to clarify few of my doubts in this regard.

In step 1 and 2, how can I ensure that the correct atom charges has been assigned for the protein as well as the ligands?

In step-2, when ligand sdf file is converting to pdbqt format, do I need to do enegy minimization for each of the lead compound in the sdf file?. If so, how can I do both the task (convering to pdbqt file and energy minimization) together for for all the lead compouds in the sdf file (~1986 nos.) in PyRx?

What could be your suggestion about runing autodock locally in my system ( Ubntu 32-bit)? or Do I need to run it with Opal web service?


Many thanks in advance

Regards
Aneesh
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aneeshcna
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Re: Help for structure-based virtual screeing

Postby sargis » Mon Feb 03, 2014 10:10 pm

aneeshcna wrote:I am new with PyRx and virtual screeing. I have installed PyRx in my Ubuntu 32-bit systems and also download sdf file of lead compounds from NCIDS database. The single sdf file contains multiple compounds (1986 compounds). As per the informations from different screncasts and blog from PyRx website, the oversall idea I got about how to do structrue-based virtual screeing with PyRx is listed below.

1. Prepare the pdbqt file for protien of interest
2. Convert ligands sdf file to pdbqt file.
3. Generate grid for the site (acvite site) of interest in the protein, where you want to dock the ligand ( run autogrid)
4. Run the auotdock and alalyze the result.

Am I going on the right direction? If yes, please hlep me to clarify few of my doubts in this regard.

Yes, this sounds right.
aneeshcna wrote:In step 1 and 2, how can I ensure that the correct atom charges has been assigned for the protein as well as the ligands?

I don't know how to ensure the correct atom charges has been assigned for the protein as well as the ligands. You will need to read the code and/or pdbqt files created. It also depend what you mean by "correct atom charges".
aneeshcna wrote:In step-2, when ligand sdf file is converting to pdbqt format, do I need to do enegy minimization for each of the lead compound in the sdf file?. If so, how can I do both the task (convering to pdbqt file and energy minimization) together for for all the lead compouds in the sdf file (~1986 nos.) in PyRx?

Energy minimization is recommended if your ligand sdf file is flat (2D). To do both the task (converting to pdbqt file and energy minimization) together you'll need to write a script.
aneeshcna wrote:What could be your suggestion about runing autodock locally in my system ( Ubntu 32-bit)? or Do I need to run it with Opal web service?

I suggest runing autodock locally on a single system or a cluster. I no longer support Opal web service code, and last I checked it wasn't working because of the changes done on Opal server side.

Thank you for using PyRx!
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