Top 10 Templates for Domain Assembly

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Top 10 Templates for Domain Assembly

Post by rhajjo »

I am using I-TASSER to generate a 3D protein model. The query amino acid sequence has a crystal structure in the PDB. However, this crystal structure isn't among the top templates for domain assembly. All top 10 templates picked by I-TASSER for domain assembly have sequences that are less similar to the query sequence (than the PDB structure that belong to the query sequence). Why is that?

I appreciate your thoughts on this.
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Joined: Tue May 04, 2021 5:04 pm

Re: Top 10 Templates for Domain Assembly

Post by jlspzw »


Our template library is PDB70, which is not an entire PDB, it takes a no-redundant PDB library with structure similarity cutoff TM-score=0.7. So it is possible that your native structure is not in the library. Since our library is not based on sequence similarity, so it is possible that the picked-up template has low sequence similarity with your native, but it should have structural similarity with your native, you can use TM-align check with it. Also if your sequence is a multi-domain protein, and each domain has a native structure, I-TASSER will try to pick up the longest templates to cover the largest domain, if no full-length templates. This is also why for multi-domain targets, some domain-level templates may not be shown in the top 10 templates. if you want to do domain assembly, and for each domain you know the structure, try our DEMO server ( if you want to do multi-domain protein modeling, try LOMETS3 ( or I-TASSER-MTD (
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