InterPro | How To Know About Domain In Protein Structure & Their Function in 5 mins | Bioinformatics
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- Опубликовано: 15 сен 2024
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InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterize them.
InterPro provides the world’s most comprehensive predictions by combining predictions from 13 member databases. This webinar defines the basic InterPro notions, concepts of protein classification and describes how InterPro ensures the accuracy of its data. This webinar also explains the different methodologies used by the InterPro member databases in their predictions and how we integrate them into the 5 different InterPro entry types: Homologous superfamily, family, domain, repeat and site. Finally, it presents some examples of different external resources using the InterPro database as an underlying resource.
The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites. Models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences (such as those arising from novel genome sequencing) in order to classify them. Each of the member databases of InterPro contributes towards a different niche, from very high-level, structure-based classifications (SUPERFAMILY and CATH-Gene3D) through to quite specific sub-family classifications (PRINTS and PANTHER).
InterPro's intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures that represent equivalent domains, sites or families are put into the same entry and entries can also be related to one another. Additional information such as a description, consistent names and Gene Ontology (GO) terms are associated with each entry, where possible.
#interproscan #protein_family #protein_classification
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You make things so much easier to learn. Thank you for the efforts.
You're very welcome!
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Happy to help
Tysm sir.. very helpful tutorial
So nice of you
i am using interpro, but my results arent like yours, it shows the entry matches to Domain of Unknown Function and in that Predicted 3 domains, cytoplasmic, transmembrane and non-cytoplasmic, all with no siginificant pdb match
If you see on your right hand side then there will be some number like IP0231098. Click on them. It will take you to the specific domain section. There will be structures of domains as well
@@bioinfoxpert yeah i did that too. No structures or any homolog to that domain as well Since i m working on novel protein with no annotations so its different for me n thats where i am stuck n tired n confused..
Yes you are right. It happens sometime
How to know the motifs functions?
Dear you can click on number present along the motifs. When you will click on them then the details of motif will come infront of you.
Can we only select to use Pfam only in interprot?
Yes you can use Pfam. It will be totally fine.
Hello sir, on my result page, there is predictions entry.. what is that?
You are very right but in case we do not hv 3D structure in PDB then then alpha fold is a good option
Interpro let you the domain which are validated in literature. Along with it based on sequence homolgy it also predicts some possible domain in your sequence. These are just predictions.
There is no domain...only predictions...how can i draw pdb and highlight domains with name in form of diagram as i have to paste it in thesis
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