How to Perform Molecular Docking in 2 mins|Protein-Ligand Docking in 2 Min|Bioinformatics Tutorial

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Bioinfoxpert

Bioinfoxpert

Күн бұрын

Пікірлер: 66
@bioinfoxpert
@bioinfoxpert 2 жыл бұрын
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@zahidbashirzargar7564
@zahidbashirzargar7564 2 жыл бұрын
Sir ,can you please explain how we can do docking of multiple ligands at same time
@rikardoss
@rikardoss Жыл бұрын
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.
@BilalAHMAD-hf4gf
@BilalAHMAD-hf4gf 3 жыл бұрын
Very informative video. Dear Sir, Can you kindly share the video of ''How to design the 3 dimensional structure of the Ligand''?''
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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
@aneelalakanwalkanwal5799
@aneelalakanwalkanwal5799 2 жыл бұрын
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
@farzadmolani7435
@farzadmolani7435 Жыл бұрын
Hi. Thanks for the video. How can someone get RMSD for each pose?
@nonhlemkhwanazi2149
@nonhlemkhwanazi2149 2 жыл бұрын
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.
@noor-ul-ainmurtaza7117
@noor-ul-ainmurtaza7117 3 жыл бұрын
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?
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
We will work on it
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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@aishashahfiquee9729
@aishashahfiquee9729 3 жыл бұрын
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
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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
@priyankasshaji1237
@priyankasshaji1237 Жыл бұрын
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.
@bioinfoxpert
@bioinfoxpert 11 ай бұрын
Dear If you are using the CB dock then you can upload 2D structures of your ligands only. Leave the rest to CBdock
@jayakumark707
@jayakumark707 3 жыл бұрын
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?
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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
@iqra4650
@iqra4650 3 жыл бұрын
Thank you sir for this easy method for docking 🌼
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
Thanks
@imrocknreeling
@imrocknreeling 3 жыл бұрын
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?
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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.
@thebiobuddy9595
@thebiobuddy9595 3 жыл бұрын
Excellent you saved us
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
If you want to learn Bioinformatics then take our course on Udemy Course Link: bit.ly/2SFH0fz The course is with 30 days Money Back Guarantee
@zahidbashirzargar7564
@zahidbashirzargar7564 2 жыл бұрын
Sir ,can you please explain how we can do docking of multiple ligands at same time
@bioinfoxpert
@bioinfoxpert 2 жыл бұрын
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@muhammadabraryousaf1062
@muhammadabraryousaf1062 3 жыл бұрын
Do we need ligand and protein preparation before uploading them?
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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.
@sanjeev1227
@sanjeev1227 11 ай бұрын
Can we dock ligand with multiple proteins with cb dock sir
@bioinfoxpert
@bioinfoxpert 11 ай бұрын
No dear you can not
@MiniTaleTerritory
@MiniTaleTerritory Жыл бұрын
Can you dock more than one ligand at a time?
@bioinfoxpert
@bioinfoxpert Жыл бұрын
No you can not do that for this you need to adopt sequential docking protocol
@MiniTaleTerritory
@MiniTaleTerritory Жыл бұрын
@@bioinfoxpert I see.
@mehwishahsan2194
@mehwishahsan2194 3 жыл бұрын
Thank you for the edifying video.
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
Thanks
@Kidsshow28
@Kidsshow28 5 ай бұрын
where is the ligand pdb video, how to make it?
@bioinfoxpert
@bioinfoxpert 4 ай бұрын
Dear Actually, its pretty easy to make ligand protein complex. Just open both in the Pymol and save them as single molecule.
@ilhambenamor97
@ilhambenamor97 Жыл бұрын
How install docking
@AmjadAli-zz1re
@AmjadAli-zz1re Жыл бұрын
Please can you share how to interpret its results
@SureshKumar-ef8xu
@SureshKumar-ef8xu 3 жыл бұрын
Can you present video on molecular dynamics simulations on webserver
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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@xufenghuang1634
@xufenghuang1634 2 жыл бұрын
Sir could you kindly tell how to get 2D picture as well?
@bioinfoxpert
@bioinfoxpert Жыл бұрын
You can use ligplus
@rbnaeem6730
@rbnaeem6730 3 жыл бұрын
Interesting info...thank you
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
Thanks rb Naeem
@diyaprajapati8300
@diyaprajapati8300 3 жыл бұрын
docking is easy by this method but i dont know how to analyse these results please help me for this
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
There is our one video regarding analysis of docking data. Please watch that video.
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
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@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
If you want to learn Bioinformatics then take our course on Udemy Course Link: bit.ly/2SFH0fz The course is with 30 days Money Back Guarantee
@afzaldanish5266
@afzaldanish5266 2 жыл бұрын
Wonderful sir Ma sha Allah
@bioinfoxpert
@bioinfoxpert 2 жыл бұрын
Thanks for liking
@Hema-et7dv
@Hema-et7dv Жыл бұрын
We want to pay for this
@bioinfoxpert
@bioinfoxpert Жыл бұрын
No this is free server
@Hema-et7dv
@Hema-et7dv Жыл бұрын
Thank you for reply
@danzingmagand
@danzingmagand 3 жыл бұрын
I love youuuu!! Gracias por la ayuda :D
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
Thanks
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
If you want to learn Bioinformatics then take our course on Udemy Course Link: bit.ly/2SFH0fz The course is with 30 days Money Back Guarantee
@NedaMAlam
@NedaMAlam Жыл бұрын
i still dont understand what is binding affinity and how this score is calculated
@bioinfoxpert
@bioinfoxpert Жыл бұрын
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.
@NedaMAlam
@NedaMAlam Жыл бұрын
@@bioinfoxpert much thanks ❤️
@pallavisangle4787
@pallavisangle4787 3 жыл бұрын
Hello sir.. How to get easily 2d diagram??
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
Thanks for your comment. You can use LigPlot. Its wonderful programme to analyze ligand protein interaction
@bioinfoxpert
@bioinfoxpert 3 жыл бұрын
If you want to learn Bioinformatics then take our course on Udemy Course Link: bit.ly/2SFH0fz The course is with 30 days Money Back Guarantee
@dayanvierabarredo2635
@dayanvierabarredo2635 11 ай бұрын
only works for very small ligands
@bioinfoxpert
@bioinfoxpert 11 ай бұрын
yes this is for small ligands only
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