Swiss-model for Protein structure prediction by homology modeling 

Glad this helped you ❤

😇😇😇

sure a lot of more analysis are being prepared and will be added very soon

same brother

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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.

Using modeller is anther option for doing homology modeling but it will do manually for you.. ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-rD8XcJaZanw.html

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. ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-UNzq8YhWXno.html ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-u9Rcwsyz0BA.html

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.

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.

@@duafatima6283 ya you can go for it its a good percentage

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 ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-rD8XcJaZanw.html

ismain template ko ise kr k protein ki structure ko build kia jata he.

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

thanks 🤗

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.

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

ya