Finding active or binding site in protein sequence
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19 months ago
kishorssf91 ▴ 10

Hi, I have a bunch of a orthologue group from eight species. I want to know the active or binding site of each protein sequence. How to find the active sites or binding sites? Or is there any software to handle this?

Protein structure • 1.1k views
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A simple google search gives you plethora of option to choose from. ‚Äč Anyway, this one is my favorite. https://zhanglab.ccmb.med.umich.edu/COACH/

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Hi, thanks for your response. I have tried with your recomanded package COACH. They informed me to provide the result within 10 hour. but its been for few days that they didnt provide the result. Moreover, i have tried SWISS-model. They provides only the structure. But actually i need to know the active site or binding motif of the selected protein. Can you please give me some other idea or recommand me other tools? Thanks again for your precious time.

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Don't worry. Sometimes the servers are busy, but you will get your results. The results are much more reliable than other websites

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Hi, I have recieved result for one of my protein sequences. Thanks.

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19 months ago

Have you already looked whether your proteins are in UniProt, and whether such sites have been annotated?

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No, i didnt check throughly the uniprot database. But in uniprot the length of homologue protein is different. And the active site number is different even for closely related species (but the particular site aa is same/proximal aa is different). Is it something like peptide length may varried species to species but reaction site aa will be the same??

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