I wanted to know how one makes these structures or how is it made and uploaded to RCSB. Is there any Lab equipment that can give information about the shape or the size of proteins? Can the Size be studied/ or scanned in one go? Will the structure be broken into multiple segments if the protein is big? Is there a structure for Casein Protein as well?
These structures are made using the technique called X-ray crystallography. Coordinate information of each atom is acquired from a snapshot structure of the protein and rendered using software to make a fully 3D structure. Larde protein is hard to work with. Check-in PDB if you can find your protein. Type the name of the protein in the search box and look for the best results. Then analyze the sequence and see if it matches your protein of interest.
Sir, how do find the wild type structure of the protein?? All structures are of mutants. Like the human myoglobin. Only one structure of a mutant is available. Which is strange given that myoglobin was one of the first structures to be identified. I hope you answer as this has been puzzling!
Hi, i wanted to ask that , you know there are multiple structures for a protein are present in pdb, Among those how can i choose the best one for my research i.e fir further docking analysis etc, Like you seee i filtered the structure based on resolution and method and even specific domain.. But still i have too many structure, which on should i choose. Your opinion will be appreciated
Why are the positions of the amino acids in the protein sequence not correct? Bovine tryspin's catalytically active serine 195 has the position 177 in the sequence on PDB.
I am not sure about the questions, I suggest if you detail the question with reference to the pdb structures, I should be able to provide the answer in more detail. What are the structures you are analyzing?
While performing a BLASTp search with protein sequence against the PDB- database you have one hit with low E-value and two hits with somewhat higher E-value. On inspection of the PDB file with the best score it turns out that this 3D structure has a rather bad resolution and misses coordinates of two loops. Describe how you can use this information to identify your protein?
You are welcome and thank you for your kind comment. I would say look at the latest submitted structures (latest publication) with the highest resolution. Here is a link that explaiins PDB data in more detail. I hope it was helpful! pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/resolution
PDB has changed a bit since this video , i want to see how many b and a helix are in a protein and it doenst show anymore on the section sequence. How do i find it ?
Sir I have a confusion that in most of the research paper there is target protein and also the inhibitor or ligand(which are proved to react with that target protein).But for the further study/analysis when I wanted to retrieve the structure of target protein ,then there are different types of same proteins.Then how to know which particular protein with specific PDB ID was mentioned during that particular research paper?
Hi Pratik, thank you for watching the video and posting your question. Your question is valide, however if you read the method section clearly the author may have mentioned the exact PDB ID of that protein used in the study. You can use that PDB ID for your research. Or you can use any structure present on PBD website of that protein. I will also download all the strucutre and analyze sequence of the proteins, aligh the struxutre using pymol to see if there is any information that I can get. In the end it depends on the requirement of the experiment. I hope the ans was helpful! Thank you!
Hello every one moe docking give multiple pictures for the same amino acid with same number of residue in peptide when checked ligand interactions, Is that normal or error occure ,cause??
Thare are couple : for e.g. although it porovides the detailed structure of the protein but protein exists in dynamic confirmations so that is just one confirmation of the protein presented in PDB. In reality protein can exsist in various other forms, those forms are missing. There are also sometimes errors in the PBD files providing incomplete structure. Some protein are hard to crystalize so their stuructures are unavailable. I hope the answer was hepful.THanks
You can use Pymol software to do that. I have a playlist on pymol please watch it. I hope that helps you. Feel free to ask if you have any issue. Thanks for your comment!
HI, please help me why when I click the 3D view coming out ' graphics card driver issue. For a list of supported browsers, refer to caniuse.com/#feat=webgl.
@@sanjutha3541 Sorry to hear that you are facing these issues. Sometimes uninstalling and installing the browser works, try that. Hopefully, it will work.
While performing a BLASTp search with protein sequence against the PDB- database you have one hit with low E-value and two hits with somewhat higher E-value. On inspection of the PDB file with the best score it turns out that this 3D structure has a rather bad resolution and misses coordinates of two loops. Describe how you can use this information to identify your protein?
Hi Stephane, thank you for your msg. I would suggest you do MSA on the protein sequence to get insight into the sequence similarities. Are you trying to find similar proteins to your target proteins? Do the MSA with the best hits. Analyze your results, after that validate in a wet lab. Since I am not familiar with your project so the experiments may differ based on your main aim. I hope my suggestion was helpful. Kepp supporting. Thanks..
Hey, this seems like a good series, very clear
Thank you !
I wanted to know how one makes these structures or how is it made and uploaded to RCSB. Is there any Lab equipment that can give information about the shape or the size of proteins? Can the Size be studied/ or scanned in one go? Will the structure be broken into multiple segments if the protein is big? Is there a structure for Casein Protein as well?
These structures are made using the technique called X-ray crystallography. Coordinate information of each atom is acquired from a snapshot structure of the protein and rendered using software to make a fully 3D structure. Larde protein is hard to work with. Check-in PDB if you can find your protein. Type the name of the protein in the search box and look for the best results. Then analyze the sequence and see if it matches your protein of interest.
Sir, how do find the wild type structure of the protein?? All structures are of mutants. Like the human myoglobin. Only one structure of a mutant is available. Which is strange given that myoglobin was one of the first structures to be identified.
I hope you answer as this has been puzzling!
I am not getting a clear view of your question, can you please explain in more detail..
Thank you so much .
Thank you for your valuable feedback 🙏
Thank you so much, i didn't know where to search proteins based on a code.
Thank you for your kind feedback 🙏
Hi, i wanted to ask that , you know there are multiple structures for a protein are present in pdb,
Among those how can i choose the best one for my research i.e fir further docking analysis etc,
Like you seee i filtered the structure based on resolution and method and even specific domain..
But still i have too many structure, which on should i choose.
Your opinion will be appreciated
Choose the one with best resolution rest depends on your objectives
Why are the positions of the amino acids in the protein sequence not correct? Bovine tryspin's catalytically active serine 195 has the position 177 in the sequence on PDB.
I am not sure about the questions, I suggest if you detail the question with reference to the pdb structures, I should be able to provide the answer in more detail. What are the structures you are analyzing?
While performing a BLASTp search with protein sequence against the PDB-
database you have one hit with low E-value and two hits with somewhat
higher E-value. On inspection of the PDB file with the best score it turns out
that this 3D structure has a rather bad resolution and misses coordinates of two
loops. Describe how you can use this information to identify your protein?
Perform hhblits of your protein in combination with homolgy modeling try to model the protein. I hope the answer was helpful. Thanks
Hello Sir, Can you please make a video how to deposit data in PDB
Good suggestion! I ll look in to it. Thank you for watching the video 🙏
Thx for video
Thank you for watching the video and sharing your thoughts ! Thank you!!
thanks sir for the video. what are the criteria to choose the best protein structure from PDB to be used as the target
You are welcome and thank you for your kind comment. I would say look at the latest submitted structures (latest publication) with the highest resolution. Here is a link that explaiins PDB data in more detail. I hope it was helpful! pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/resolution
Sir, I want to protein pdb only so how can i delete ligand part that attach with protein.
Specifically select the ligand
PDB has changed a bit since this video , i want to see how many b and a helix are in a protein and it doenst show anymore on the section sequence. How do i find it ?
You are absolutely right, I will try to make an updated video on the same 👍🏼🙏
What is selection criteria for Protein selection from PDB for Docking.
Depends on many factors, such as the disease you targeting, active site containing, allosteric inhibitor screening
Sir I have a confusion that in most of the research paper there is target protein and also the inhibitor or ligand(which are proved to react with that target protein).But for the further study/analysis when I wanted to retrieve the structure of target protein ,then there are different types of same proteins.Then how to know which particular protein with specific PDB ID was mentioned during that particular research paper?
Hi Pratik, thank you for watching the video and posting your question. Your question is valide, however if you read the method section clearly the author may have mentioned the exact PDB ID of that protein used in the study. You can use that PDB ID for your research. Or you can use any structure present on PBD website of that protein. I will also download all the strucutre and analyze sequence of the proteins, aligh the struxutre using pymol to see if there is any information that I can get. In the end it depends on the requirement of the experiment. I hope the ans was helpful! Thank you!
Hello every one
moe docking give multiple pictures for the same amino acid with same number of residue in peptide when checked ligand interactions, Is that normal or error occure ,cause??
Everyone please provide your response 🙏🏻
Nice video. What are some limitations of PDB?
Thare are couple : for e.g. although it porovides the detailed structure of the protein but protein exists in dynamic confirmations so that is just one confirmation of the protein presented in PDB. In reality protein can exsist in various other forms, those forms are missing. There are also sometimes errors in the PBD files providing incomplete structure. Some protein are hard to crystalize so their stuructures are unavailable. I hope the answer was hepful.THanks
@@BasicScienceSeries Thank you sm
Hi! Is there any way to know how many domains a protein has from the PDB?
Yes there are many ways, please download the structure and analyze its 3d structure for domains using software like pymol
hello, how do you know which one of these domains to use?
That information is based on the available literature in how these protein function. What is your protein of interest?
from where u get code? for your protein
Search the name of your protein in PDB and look for the code. What is the protein that you are working on?
May I ask how to look for sequence chain view in pdb? I believe the PDB that is used currently is in a different version compared to sir.
They keep on updating the software interface. I hope it worked for you. Please let me know if I can be of any help 🙏
Hi I was hoping you can help me is there anyway we can put a legend with color identifying each unit?
You can use Pymol software to do that. I have a playlist on pymol please watch it. I hope that helps you. Feel free to ask if you have any issue. Thanks for your comment!
not able to find sequence chain view. please help
Look for the small s button on the right corner. Click it and you should see the sequence !
Thanks for the reply. But unfortunately the whole page output I am getting is different than shown here @9.55
@@anjusree4664 Interesting, I wish I could see what you are seeing.
How many year to do the course
Probably few more 🤭
@@BasicScienceSeries oh🙄
HI, please help me why when I click the 3D view coming out ' graphics card driver issue.
For a list of supported browsers, refer to caniuse.com/#feat=webgl.
It should work with an updated version of google chrome.
@@BasicScienceSeries but one day before able to open. Suddenly the next day error.
@@BasicScienceSeries appreciate your reply so much so other than updated google chrome no other way to solve this ?
@@sanjutha3541 Sorry to hear that you are facing these issues. Sometimes uninstalling and installing the browser works, try that. Hopefully, it will work.
@@BasicScienceSeries thank u so much for the replies ya ❤
While performing a BLASTp search with protein sequence against the PDB-
database you have one hit with low E-value and two hits with somewhat
higher E-value. On inspection of the PDB file with the best score it turns out
that this 3D structure has a rather bad resolution and misses coordinates of two
loops. Describe how you can use this information to identify your protein?
Hi Stephane, thank you for your msg. I would suggest you do MSA on the protein sequence to get insight into the sequence similarities. Are you trying to find similar proteins to your target proteins? Do the MSA with the best hits. Analyze your results, after that validate in a wet lab. Since I am not familiar with your project so the experiments may differ based on your main aim. I hope my suggestion was helpful. Kepp supporting. Thanks..