Questions tagged [domains]

A discrete region of a protein with a defined structure. A domain usually has a specific function. A protein is usually made up of one or several domains. The same domain can occur in different proteins.

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Convert .smp downloaded from NCBI CDD into HMM(.hmm) file [closed]

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
0 votes
1 answer
42 views

Can anyone point me towards a HiC Dataset with domains of high confidence?

is there a dataset online containing a HiC contact matrix and file with TAD boundary locations, which were generated, either by hand or automated, with high accuracy? Although I already used programs ...
1 vote
1 answer
102 views

ipfam or pfam domain-domain interactions

I'd like to download domain-domain interactions that were in ipfam (which doesn't seem to be up-and-running anymore). for an example of what I would like to be able to download via ftp or another ...
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5 votes
0 answers
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Map domain names from UniProt bed files to domain accessions

I want to get a bed file mapping human protein domains to the human genome. UniProt actually offers such a thing here. The problem, however, is that the file doesn't include any kind of domain ...
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5 votes
3 answers
988 views

Obtaining all protein sequences with a particular domain architecture from Pfam

I want to get the alignment of chain A of 1kf6 (PDB ID) from the pfam database here. This protein chain has two main domains (FAD_binding_2 and Succ_DH_flav_C). In pfam there is a link to one of ...
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