Hello, dear researchers
I hope you are well
Is there a tool that gives 3D coordinates for each amino acid?
The protein sequence is in FASTA format
An example sequence is:
>1a81A.txt
SANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKI
Thank you for your guidance
Hello
Yes, there are tools available that can provide 3D coordinates for each amino acid in a protein based on its sequence in FASTA format. One such tool is SWISS-MODEL.
SWISS-MODEL is a protein structure homology-modeling server that allows you to input a protein sequence and obtain a 3D model of the protein.
Other tools, such as MODELLER, also provide similar functionality for protein structure prediction. It's always a good idea to compare the results from different tools and assess the reliability of the models generated.
Is the structure of your protein known? If yes, download the PDB and the coordinates are within the file. If no, use AlphaFold to predict the structure or any other tool (Rosetta, SwissModel, Modeller). By itself, FASTA format does not give you the structure of your sequence, just the sequence itself.
If the structure of the protein is known, you can download it from https://www.rcsb.org/. Otherwise, you can use ESMFold at https://github.com/facebookresearch/esm.
DEAR Sargol Mazraedoost
Thanks for sharing , Is it possible to share the suggested tool link?Thanks so much