8 votes
Accepted

How to extract RNA sequence and secondary structure restrains from a PDB file

I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various ...
Marcin Magnus's user avatar
6 votes
Accepted

Do any publicly available databases detail protein structure and functional domains?

Some of this information (at least some domains, active sites, etc) is available from UniProt. If you want to download their whole database, you can search without specifying any terms and then click ...
Nils's user avatar
  • 315
5 votes
Accepted

What tool RCSB and AlphaFold use to visualize 3D structures?

Different criteria give different rankings. Mol* (read molstar with trilled rhotic R according to the given IPA) is the newest, is used by the RCSB PDB and can ...
5 votes
Accepted

JSmol - hide "JSmol" logo

OK, I got an answer here. Use: frank off to get:
Marcin Magnus's user avatar
4 votes

How to extract RNA sequence and secondary structure restrains from a PDB file

Context The PDB file format is a fixed-column file format designed in 1970s for storing structural models of macromolecules. The format has been around for long time, has many uses, and although it ...
marcin's user avatar
  • 1,261
4 votes

How to find hairpin loop structure in a large set of long non coding RNA transcripts

For the first question: "how many of long non coding can make hairpin loop structure?" The easiest thing to would be to run your sequences through an RNA secondary structure prediction tool. There's ...
juniper-'s user avatar
  • 890
3 votes

Coronavirus RNA structures?

To add a more complete answer: the current coronavirus is closely related to the SARS virus that caused the outbreak in 2004, and on which much research has been done. Here is a general review of the ...
Roger V.'s user avatar
  • 381
3 votes

Practical use of RNA structure

Please look up flavivirus 'double loops' as you described them previously (post for "Coronavirus RNA') and associated RNA secondary structure anomalies for dengue virus and associated vaccine (...
M__'s user avatar
  • 12.1k
3 votes

Do any publicly available databases detail protein structure and functional domains?

EnsEMBL also has this. Search for your gene of interest, choose your transcript, go to the page of its protein product(s), and select "Domains & Features" from the right-hand menu (using human p53 ...
terdon's user avatar
  • 9,846
2 votes

Understanding ViennaRNA RNAdistance scoring table

Ok, the answer was right here and I missed it, posting it in case anyone else will do the same mistake as me in the future. ...
Eli Zatlawy's user avatar
2 votes

Protein misfolding

Excellent question! I would recommend that you start with an NIH resource at the National Library of Medicine (NLM). PubMed (https://pubmed.ncbi.nlm.nih.gov/) provides search capabilities across the ...
BalooRM's user avatar
  • 123
1 vote

Is loss/gain of function reflected in RNA-seq transcript counts?

Short answer Since the effects of any given mutation is so context-dependent (and deciding which effects matter will change between researchers), the process of "variant annotation" is ...
James Hawley's user avatar
  • 1,384
1 vote

How to extract RNA sequence and secondary structure restrains from a PDB file

If you know how to use python: 1 - Download the ModeRNA module from here and install 2 - from a python IDLE execute: ...
Ivan Castro's user avatar

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