Thank you very much dear doctor ashfaq, i have many questions About rdkit can I install locally in my machine Can it generates new molecule by its library with specific threshold and record ? Hair can I use more than one data like zinc and chembl?
Dear ES-yd1ze yes you can install rdkit locally. Based on the system architecture you can either use appropriate command, like "pip install rdkit". Next, yes rdkit can generate smiles to a structure. So what ever you want to bring changes, please bring them in smiles. Also, you can use chemdraw, and the structure you draw can be saved in smiles. Yes, you can use data from zinc or chembl etc but for that please keep the file formate uniform. Also, when you are using data from different databases, be careful because at times, people are treating redundant data from different databases. Regards
thanks alot..Can you make video on RNA targeted drugs? where RNA is a target not a protein..I have one more question..Does alpha fold 3 can be used for Docking?..please reply me Sir..
@JodhaManjinder, you can modelled or dock protein-protein, protein-RNA, protein-DNA, Protein-Peptides, and some smaller organic molecules, like ADP, ATP etc. If you are asking for docking of every ligand of your choice with DNA, RNA or protein, then NO. I have covered a detailed video on AlphaFold3, you can watch it here, ruclips.net/video/iGGby6zavAY/видео.htmlsi=PbAKlQAhGtgxMO1f. I will try to make videos using RNA as a target, but first i will need to gather some literature, therefore, it may not be possible in near future. Thanks for watching and taking interest.
No one can provide a confident answer for the question you ask. Based on larger library, one would say yes, but quantity doesn't guarantee the chances of success. On the other hand, quantity do increase the Expected factor, means it increase the chances of good compounds to be hit as positive.
Assalamualaikum sir!!! Sir, let i have the target protein and yet i didn't perform virtual screening of compounds, in that case should i need to find common compounds if yes, then how would i know about the reference compound I'll use?
If you want to find common compounds, you can do without reference also. The algorithm will provide you different clusters, now select some compounds from every cluster for virtual screen. So in the above case you didn't employee the use of a reference compound.
I think this is most likely and easiest way to screening for compound ❤…thank you sir g❤
Keep shining sir❤
Literally you're light to darkness 😊
Thanks for good words. It motivates me to bring better stuffs
Interesting
Thank you very much dear doctor ashfaq, i have many questions
About rdkit can I install locally in my machine
Can it generates new molecule by its library with specific threshold and record ?
Hair can I use more than one data like zinc and chembl?
Dear ES-yd1ze yes you can install rdkit locally. Based on the system architecture you can either use appropriate command, like "pip install rdkit". Next, yes rdkit can generate smiles to a structure. So what ever you want to bring changes, please bring them in smiles. Also, you can use chemdraw, and the structure you draw can be saved in smiles. Yes, you can use data from zinc or chembl etc but for that please keep the file formate uniform. Also, when you are using data from different databases, be careful because at times, people are treating redundant data from different databases.
Regards
thanks alot..Can you make video on RNA targeted drugs? where RNA is a target not a protein..I have one more question..Does alpha fold 3 can be used for Docking?..please reply me Sir..
@JodhaManjinder, you can modelled or dock protein-protein, protein-RNA, protein-DNA, Protein-Peptides, and some smaller organic molecules, like ADP, ATP etc. If you are asking for docking of every ligand of your choice with DNA, RNA or protein, then NO. I have covered a detailed video on AlphaFold3, you can watch it here, ruclips.net/video/iGGby6zavAY/видео.htmlsi=PbAKlQAhGtgxMO1f.
I will try to make videos using RNA as a target, but first i will need to gather some literature, therefore, it may not be possible in near future.
Thanks for watching and taking interest.
Can you please make a video on topic Regeneration in humans ; Analysis by Bioinformatics tools etc
@abubakarraja, sorry for late response. The next video is based on your request. Thanks for watching
@@Bioinformaticsinsights Thank you so much dear Sir ! . I am curiously waiting for it 😍
Sir if i just wish to find a good inhibitor drug against my target protein, screening a large library of such compounds wil be enough?
No one can provide a confident answer for the question you ask. Based on larger library, one would say yes, but quantity doesn't guarantee the chances of success. On the other hand, quantity do increase the Expected factor, means it increase the chances of good compounds to be hit as positive.
Assalamualaikum sir!!!
Sir, let i have the target protein and yet i didn't perform virtual screening of compounds, in that case should i need to find common compounds if yes, then how would i know about the reference compound I'll use?
If you want to find common compounds, you can do without reference also. The algorithm will provide you different clusters, now select some compounds from every cluster for virtual screen. So in the above case you didn't employee the use of a reference compound.