Virtual Screening | Ligands Preprocessing With Free Tools || Drug Discovery || P2c-1

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#virtualscreening #drugdiscovery #ligandpreprocessing #ligandpreparation #datawarrior #openbabel #gypsumdl
How to prepare and preprocess your ligand's library for Target Based Virtual Screening? This series of videos consists of three parts. This is part 2. Part 2 has been subdivided into three videos. This is the third video of part 2. In this part you will see how to generate stereoisomer, conformers, cis/trans isomers, how to add hydrogens, partial charges, and how to filter (duplicate removal) and convert ligands library format.
for part 1 go to: • Virtual Screening | Lo...
for part 2a go to: • Virtual Screening | Li...
for part 2b go to: • Virtual Screening | Li...
For Next Part go to: • Virtual Screening | Ta...
For all the videos about Drug Designing go to: • Virtual Screening | Li...
For discovery studio visualizer tutorials go to: • Download and Installat...
For bioinfomatics videos go to: • Learn MEGA in 7 Minute...
For life sciences lessons go to: • Identify Plant Species...
For other educational videos go to: • Nitrogenous bases stru...
For all the playlists: www.youtube.co...
For primer designing go to: • Primer Designing | Usi...
For Biopython: • Biopython Course | Dow...

[@ivanbogdanov8545]

I don't know who you are, I don'teven know what are you doing, but I THANK YOU FROM THE BOTTOM OF MY HEART for these tutorial videos!!!

[@roughcooking]

Many many thanks for this detailed video👍👍👍👍

[@RoshanAliAcademy]

You are welcome

[@roughcooking]

@@RoshanAliAcademy so many scientific community didn't consider bioinformatics as important field. Nowadays it shows its dependency and people's like you make it easier. Thank u

[@RoshanAliAcademy]

@@roughcooking Its all due to your love dear....

[@rubisco3384]

good video. Thank you. can you do a tutorial of 3dqsar studies and pharmacophore modeling

[@ShivanshGupta6]

Thank you for your videos..very simple content for beginners..can you tell me how can we do simulations in different pH environment

[@ShivanshGupta6]

@@RoshanAliAcademy
Thank you for your suggestion.
My point is if we want to do simulation at pH 4.0 for my protein, how can I change protein residue at pH 4.0.

[@joyli6707]

Hi, Thank you so much for these detailed videos.
For the DataWarrior, I see in the video, you put that it can add hydrogen, creates 3D and conformers. I had some issue with open babel installation, I was wondering if you can specify if I can use functionalities in DataWarrior to generate protonated 3D structure from 2D SDF files. Thanks

[@RoshanAliAcademy]

You are welcome dear. Yes, DataWarrior does have functionalities to generate protonated 3D structures from 2D SDF files. Here's how you can typically approach this in DataWarrior:
Import your SDF file: Start by importing your 2D SDF file into DataWarrior. SDF (Structure Data File) is a standard format used for representing chemical structures and associated data.
Prepare for 3D generation: Once your molecule is loaded, ensure that it has all the necessary information required for 3D structure generation. This typically includes atomic coordinates and bond information.
Generate 3D structures: DataWarrior can use various methods to generate 3D structures, including protonation. It often utilizes external tools or plugins for this purpose, depending on the version and plugins installed.
Adjust protonation and optimization: After generating the initial 3D structure, you may need to adjust protonation states or optimize the structure further to ensure it accurately represents the molecule in its intended state.
Save the 3D structure: Once satisfied with the 3D structure, you can save it back into a suitable format for further analysis or visualization.

[@ChibiQilin]

I see in the example command for filtering with obabel by molecular weight you use the filter "MW

[@RoshanAliAcademy]

Yes, please read lipinski rules of five

[@ChibiQilin]

@@RoshanAliAcademy Thank you, I'll look this up!

[@khyasemin6318]

Thank you very much ,it is useful content
Can I get the powerpoint presentation from you ?

[@khyasemin6318]

Also we need to make tutorial about MOE software for docking
And the processing is difficult with commands
If there any free software make all process easy??

[@thebegginer5325]

i have more number of zinc sdf files in that case do we have to type all the names in the command to merge them??

[@rudragoudabiradar2058]

Is it really necessary to build conformers of ligand bcoz while docking it is time consuming

[@Quran_recitation-]

waste time consuming videos