amazing videos. Will there be any videos about molecular dynamics simulation amber/Gromacs..i was really hoping for it you have an amazing skill of explanation
You can use "swiss model" if they have any template with similarity of at least 70%. otherwise you have to use "itasser" For any structure which dont have any sufficient similarity of at least 70℅ with a template( any other predicted protein structure at pdb or any other database).
Ya sure. Obtain the unknown DNA sequence: First, you need to obtain the DNA sequence you want to analyze. This sequence can be obtained through various methods such as PCR, sequencing, or other experimental techniques.
Mam in which condition we prepare model by Homolgy modeling if the structure is already present in PDB database then we can use it or we will prepare it by modeling
@@wasifullahdawar6962 if its already available at PDB than you dont need to predict it from any method at all. PDB is the best database who predict perfect structures already.
@@annamhussainofficial2535 But as I know Alphafold structure is also a AI Structure, not the real one. Why would I predict model based on a Predicted AI structure! please let me know.
Yes exactly. But you can use template structures of your own sequence if you have. It will build structure of your given sequence by using your template.
hmen sare parameters ko ek sath consider krna hota he apki GMQE value to achi aa ri he but apki identity bht km aa ri he and query coverage b matter krti he so i suggest k template k liye at least 60-70% identity to ho then you can go with it.
the maximum sequence length for protein modeling on Swiss-Model was around 1500 to 2000 amino acids you can use modeller for large sequence length as MODELLER typically doesn't have a strict fixed limit on sequence length, but larger proteins may require more computational resources and time for modeling.
Thank you for your explanation maam. Please add more videos. Can you please suggest how to use Linux operating systems while doing these bio informatics works? Waiting for your video explanations.
Well, in that case you can not use homology modeling. Then you need to chose the ab inotio method i. e. Predict structure from scratch without template. I have discussed ab initio method in this video. th-cam.com/video/UNzq8YhWXno/w-d-xo.html th-cam.com/video/u9Rcwsyz0BA/w-d-xo.html
@@annamhussainofficial2535 i am confused at one point you said prefer to take a structure that has been validated by experimental studies and the method for my template is alphafold.... kindly clear this
@@hibabukhary-q4f for homology modeling if you have more than 70℅ identity than you can confidently go for swissmodel in order to predict your structure but if its not. than you have to swtich at other ab initio methods like itasser and than these structures need to be validate also becaz their quility is poor and rough so we have to enhance its quality. And you can also enhance the quality of those structures which are predicted through homology modeling if its quality is poor.
mam how do we find sequence which don't have structure and then how we find the template which have 30 plus similarity please tell me asap and I am from India ur other videos help me a lot thank. u for that please resolve my query
@@hhh-mp8kw for structure please check in pdb and other structural databases if the structure is predicted than you will get there but in case the structure is unpredicted than you could not find in any database.
The link for this sequence is here: www.uniprot.org/uniprotkb/P03954/entry#sequences now the interface of UniProt has changed completely. now we can either copy and download but before two years we can get FASTA sequence in this form as it is shown in the video
Sure a lot of contents specifically at structure modelling is being prepared and will be uploaded very soon with excellent graphics. Actually i try to put a lot or at least maximum effort from my side before uploading any lecture which takes time as i m also a full time university teacher also. Only barrier for delay is just the time management but don't worry i m trying hard and will upload its new lectures very soon
I am new to bioinformatics, my question is what if % identity and Query coverage is less but the GMQE and Qmean score is good?, which factors are more important than the other when deciding on a good model? Again what does it mean when your swiss model has no QSQE score?
Identity and query coverage are the top parameters which are considered first then we will go for other parameters. For model we need to fist check identity and query coverage parameters
Thank you for making bioinformatics somewhat easy! God bless your good work.
This lecture was so so clear cut. Loved it.❤❤❤
Glad this helped you ❤
One of the best lecture to understand about swiss model
amAZING
amazing videos. Will there be any videos about molecular dynamics simulation amber/Gromacs..i was really hoping for it you have an amazing skill of explanation
Thanks for your appreciation, yes molecular dynamics simulations will be covered in future videos.
how can we make the structures which are not predicted,,. they are not predicted before
You can use "swiss model" if they have any template with similarity of at least 70%. otherwise you have to use "itasser" For any structure which dont have any sufficient similarity of at least 70℅ with a template( any other predicted protein structure at pdb or any other database).
Thank you ma'am ❤❤
If there is no template matching found while uploading the sequence, then what should be done?
@@nikitasrivastava2470 than you have to change the method to ab initio because this tool is for homology modeling where we always have a template.
Tomorrow is my bioinformatics exam.and your video is savings my ass. so thank you.take love mam❤
😇😇😇
Hey there! I am new in bioinformatics.. just have this subject for one semester.. Can you please guide me from where can i get the unknown sequence
Ya sure.
Obtain the unknown DNA sequence: First, you need to obtain the DNA sequence you want to analyze. This sequence can be obtained through various methods such as PCR, sequencing, or other experimental techniques.
Mam in which condition we prepare model by Homolgy modeling if the structure is already present in PDB database then we can use it or we will prepare it by modeling
@@wasifullahdawar6962 if its already available at PDB than you dont need to predict it from any method at all. PDB is the best database who predict perfect structures already.
@@annamhussainofficial2535 Ok Mam Thanks
@@annamhussainofficial2535 Ok Thank You Mam
What are the other tool?
Using modeller is anther option for doing homology modeling but it will do manually for you..
th-cam.com/video/rD8XcJaZanw/w-d-xo.html
what if model match 80% above with alphafold structure! Shall I build model based on it?
@@wwayimran6911 yes of course you can built
@@annamhussainofficial2535 But as I know Alphafold structure is also a AI Structure, not the real one. Why would I predict model based on a Predicted AI structure! please let me know.
@@wwayimran6911 okay you cannot use structure. You have to use sequence for that prediction.
Yes exactly. But you can use template structures of your own sequence if you have. It will build structure of your given sequence by using your template.
This database is for building structure from template not for refining or enhancing the quality of your already predicted structure.
Amazing lecture mam
Asalamu Alaikum
Mere template ki GMQE value 0.15 arhi h, identity 49.12, coverage 0.19..
please suggest kya m yh template select krskti hn???
hmen sare parameters ko ek sath consider krna hota he apki GMQE value to achi aa ri he but apki identity bht km aa ri he and query coverage b matter krti he so i suggest k template k liye at least 60-70% identity to ho then you can go with it.
agr GMQE kivalue zero ho to phr kia template le skty
@@ahmadrajpoot6943 yes
My a.a sequence is more then 5000? What to do in this case?
the maximum sequence length for protein modeling on Swiss-Model was around 1500 to 2000 amino acids
you can use modeller for large sequence length as MODELLER typically doesn't have a strict fixed limit on sequence length, but larger proteins may require more computational resources and time for modeling.
you can use modeller for this sequence by using my this lecture th-cam.com/video/rD8XcJaZanw/w-d-xo.html
Thank you for your explanation maam. Please add more videos. Can you please suggest how to use Linux operating systems while doing these bio informatics works? Waiting for your video explanations.
sure a lot of more analysis are being prepared and will be added very soon
same brother
What if percentage identity is 100% but query coverage is 19%, can I do homology modelling for this protein?
No if query coveraye if 18 ℅ it means that similarity with the sequence is just nothing
Query coverage must be 90 to 100℅ and indentity must be 70 to 80% at least then the sequence fall in the catogary for homology modelling
Thank you very much for your response. Then should I go for ab initio modelling?
@@andaleebfatima1877 yes you can use i tasser.
Mam how to find target sequence which structure is not predicted please explain mam please
Isme inhibitor nhi hota kya after modelling???
ismain template ko ise kr k protein ki structure ko build kia jata he.
Hi, i'm getiing 0.59 in GMQE and 75 identity, is that okay?
@@duafatima6283 ya you can go for it its a good percentage
Thank you mis
😇
IF identity and sequence alignment is less than 30 percentage what should we do
Well, in that case you can not use homology modeling. Then you need to chose the ab inotio method i. e. Predict structure from scratch without template. I have discussed ab initio method in this video.
th-cam.com/video/UNzq8YhWXno/w-d-xo.html
th-cam.com/video/u9Rcwsyz0BA/w-d-xo.html
my query cover is 98, identity is 71%, method is alphafold v2, GMQE is 0.87 ... can i take this template
@@hibabukhary-q4f yes of course you can take.
@@annamhussainofficial2535 i am confused at one point you said prefer to take a structure that has been validated by experimental studies and the method for my template is alphafold.... kindly clear this
@@hibabukhary-q4f for homology modeling if you have more than 70℅ identity than you can confidently go for swissmodel in order to predict your structure but if its not. than you have to swtich at other ab initio methods like itasser and than these structures need to be validate also becaz their quility is poor and rough so we have to enhance its quality. And you can also enhance the quality of those structures which are predicted through homology modeling if its quality is poor.
mam how do we find sequence which don't have structure and then how we find the template which have 30 plus similarity please tell me asap and I am from India ur other videos help me a lot thank. u for that please resolve my query
You can find sequence from NCBI and from BLAST database.
@@annamhussainofficial2535 mam how we will know it's structure is not predicted mam can u please explain in steps how to do it please mam
Please mam explain this step in steps
@@hhh-mp8kw for structure please check in pdb and other structural databases if the structure is predicted than you will get there but in case the structure is unpredicted than you could not find in any database.
well explained
Which protein you used ??
The link for this sequence is here: www.uniprot.org/uniprotkb/P03954/entry#sequences
now the interface of UniProt has changed completely. now we can either copy and download but before two years we can get FASTA sequence in this form as it is shown in the video
Mam plz make a video on how we will find the active site of a protein and how we will do modeling of protein by Alpha fold3
Sure a lot of contents specifically at structure modelling is being prepared and will be uploaded very soon with excellent graphics. Actually i try to put a lot or at least maximum effort from my side before uploading any lecture which takes time as i m also a full time university teacher also. Only barrier for delay is just the time management but don't worry i m trying hard and will upload its new lectures very soon
@@annamhussainofficial2535 Ok Mam I m waiting
I am new to bioinformatics, my question is what if % identity and Query coverage is less but the GMQE and Qmean score is good?, which factors are more important than the other when deciding on a good model?
Again what does it mean when your swiss model has no QSQE score?
Identity and query coverage are the top parameters which are considered first then we will go for other parameters. For model we need to fist check identity and query coverage parameters
@@annamhussainofficial2535 thank you very much
👌
Thanks
👍
Great
nice explanation miss
thanks 🤗
Are you from Pakistan? I think you are speaking Urdu
ya