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Is necessary to prepare the protein? i mean, what if the pdb file have a ligand included? one should take that manually or the server makes that?. Great video also.
Dear Bilal, Many thanks for your comment and sorry for late reply. Yes sure we will make a video about designing of 3D structure of protein. By the way, we have a one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
if we extract compound from plant and then check these compounds activity against breast cancer and cervical cancer then how to find related proteins for these ligand
Hi Sir, I doing my research in Chemistry. For docking I got only 2D structure of ligand in Pubchem. Can you please tell me how to find 3D structure of ligands.
How a Ligand is selected from among 1000 of Ligand available in PDB database for a particular protein inhibition? Is it like a random selection or do we need to follow any specific rule?
Dear Jayakumar, Many thanks for your reply. Sorry for being late. There is one technique which is known as virtual drug screening. Normally this technique is used to select the best possible ligand. By the way, we have one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
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Dear Aisha, Sorry for late reply. Both are reliable. You can use any of them. Yes we personally published the CB dock data. By the way, we have a one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
No, in case of CB dock there is no need of any specific preparation. Yes, it will be great if you minimize the energy of your ligands and protein before docking but its not mandatory.
Hi loved your video but can u tell how to decrease size of the ligand, i tried mol2, mol, pdb, sdf all these formats but all of them are above 15 kb. Can please help how to compress the file size of these formats?
Dear @Shah Faisal, sorry for the late reply. We were busy uploading our course on Udemy, therefore, could not pay attention to your comment. First of all, many thanks for your love. Secondly, normally ligands are small molecules having a size of less than 15Kb. I wonder why your file size is more than 15Kb. Can you please check that there is only a single pose of ligand in your file? Its very unusual to have a so much large size of ligand.
Binding affinity is a measure of the strength of the interaction between two molecules, typically a ligand (small molecule) and a receptor (large molecule). A high binding affinity indicates a strong interaction and a low binding affinity indicates a weak interaction. The binding affinity score is typically expressed as the dissociation constant (Kd), which represents the concentration of the ligand required to occupy 50% of the receptor sites. Lower Kd values indicate higher binding affinity.
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Sir ,can you please explain how we can do docking of multiple ligands at same time
Is necessary to prepare the protein? i mean, what if the pdb file have a ligand included? one should take that manually or the server makes that?. Great video also.
Very informative video. Dear Sir, Can you kindly share the video of ''How to design the 3 dimensional structure of the Ligand''?''
Dear Bilal,
Many thanks for your comment and sorry for late reply. Yes sure we will make a video about designing of 3D structure of protein.
By the way, we have a one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
if we extract compound from plant and then check these compounds activity against breast cancer and cervical cancer then how to find related proteins for these ligand
Hi. Thanks for the video. How can someone get RMSD for each pose?
Hi Sir, I doing my research in Chemistry. For docking I got only 2D structure of ligand in Pubchem. Can you please tell me how to find 3D structure of ligands.
Dear If you are using the CB dock then you can upload 2D structures of your ligands only. Leave the rest to CBdock
How a Ligand is selected from among 1000 of Ligand available in PDB database for a particular protein inhibition? Is it like a random selection or do we need to follow any specific rule?
Dear Jayakumar, Many thanks for your reply. Sorry for being late. There is one technique which is known as virtual drug screening. Normally this technique is used to select the best possible ligand. By the way, we have one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
Does anyone know how to do the CB-Dock analysis, as in what does yellow, blue and grey dash lines represents in terms of interaction bondings. Thanks.
Thank you sir for this easy method for docking 🌼
Thanks
Sir ,can you please explain how we can do docking of multiple ligands at same time
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Excellent you saved us
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Can you please tell me wheather CB dock is more relaible or Auto dock viena? I want accurate results, are the results of cb dock are publishable
Dear Aisha, Sorry for late reply. Both are reliable. You can use any of them. Yes we personally published the CB dock data. By the way, we have a one very interesting course available at udemy to learn bioinformatics. There is a good amount of information there. We hope you will like to join us. Please click below to get access www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
Please can you share how to interpret its results
Do we need ligand and protein preparation before uploading them?
No, in case of CB dock there is no need of any specific preparation. Yes, it will be great if you minimize the energy of your ligands and protein before docking but its not mandatory.
Thank you for the edifying video.
Thanks
where is the ligand pdb video, how to make it?
Dear Actually, its pretty easy to make ligand protein complex. Just open both in the Pymol and save them as single molecule.
Is this online server allows the docking of DNA with ligand attach on nanoparticle?
or any other online server which also give rmsd data as well?
We will work on it
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How install docking
Hi loved your video but can u tell how to decrease size of the ligand, i tried mol2, mol, pdb, sdf all these formats but all of them are above 15 kb. Can please help how to compress the file size of these formats?
Dear @Shah Faisal, sorry for the late reply. We were busy uploading our course on Udemy, therefore, could not pay attention to your comment. First of all, many thanks for your love. Secondly, normally ligands are small molecules having a size of less than 15Kb. I wonder why your file size is more than 15Kb. Can you please check that there is only a single pose of ligand in your file? Its very unusual to have a so much large size of ligand.
Sir could you kindly tell how to get 2D picture as well?
You can use ligplus
Can you present video on molecular dynamics simulations on webserver
Dear there are few website but they can not provide enough time of simulations. Max 2ns time is allowed for simulation which is obviously not enough
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Can you dock more than one ligand at a time?
No you can not do that for this you need to adopt sequential docking protocol
@@bioinfoxpert I see.
Can we dock ligand with multiple proteins with cb dock sir
No dear you can not
docking is easy by this method but i dont know how to analyse these results please help me for this
There is our one video regarding analysis of docking data. Please watch that video.
ruclips.net/video/jFmAemgY0So/видео.html
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Interesting info...thank you
Thanks rb Naeem
We want to pay for this
No this is free server
Thank you for reply
i still dont understand what is binding affinity and how this score is calculated
Binding affinity is a measure of the strength of the interaction between two molecules, typically a ligand (small molecule) and a receptor (large molecule). A high binding affinity indicates a strong interaction and a low binding affinity indicates a weak interaction.
The binding affinity score is typically expressed as the dissociation constant (Kd), which represents the concentration of the ligand required to occupy 50% of the receptor sites. Lower Kd values indicate higher binding affinity.
@@bioinfoxpert much thanks ❤️
Hello sir..
How to get easily 2d diagram??
Thanks for your comment. You can use LigPlot. Its wonderful programme to analyze ligand protein interaction
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Wonderful sir
Ma sha Allah
Thanks for liking
only works for very small ligands
yes this is for small ligands only
I love youuuu!! Gracias por la ayuda :D
Thanks
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